← Back to variant description
GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 8-140023955-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=140023955&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TRAPPC9",
"hgnc_id": 30832,
"hgvs_c": "c.2702G>A",
"hgvs_p": "p.Ser901Asn",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -7,
"transcript": "NM_001374682.1",
"verdict": "Benign"
},
{
"benign_score": 3,
"criteria": [
"BP4_Moderate",
"BP6"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000289741",
"hgnc_id": null,
"hgvs_c": "n.1739G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -3,
"transcript": "ENST00000698172.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1",
"acmg_score": -7,
"allele_count_reference_population": 96,
"alphamissense_prediction": null,
"alphamissense_score": 0.2594,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"chr": "8",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " autosomal recessive 13,Inborn genetic diseases,Intellectual disability,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.08974000811576843,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1148,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6899,
"cdna_start": 2797,
"cds_end": null,
"cds_length": 3447,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001160372.4",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000438773.4",
"protein_coding": true,
"protein_id": "NP_001153844.1",
"strand": false,
"transcript": "NM_001160372.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1148,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6899,
"cdna_start": 2797,
"cds_end": null,
"cds_length": 3447,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000438773.4",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001160372.4",
"protein_coding": true,
"protein_id": "ENSP00000405060.3",
"strand": false,
"transcript": "ENST00000438773.4",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 991,
"aa_ref": "S",
"aa_start": 737,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3693,
"cdna_start": 2211,
"cds_end": null,
"cds_length": 2976,
"cds_start": 2210,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000520857.5",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2210G>A",
"hgvs_p": "p.Ser737Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000430116.1",
"strand": false,
"transcript": "ENST00000520857.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2021,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000521667.5",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "n.1086G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000521667.5",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1155,
"aa_ref": "S",
"aa_start": 901,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6920,
"cdna_start": 2818,
"cds_end": null,
"cds_length": 3468,
"cds_start": 2702,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_001374682.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2702G>A",
"hgvs_p": "p.Ser901Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001361611.1",
"strand": false,
"transcript": "NM_001374682.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1155,
"aa_ref": "S",
"aa_start": 901,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4300,
"cdna_start": 2818,
"cds_end": null,
"cds_length": 3468,
"cds_start": 2702,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000889106.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2702G>A",
"hgvs_p": "p.Ser901Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559165.1",
"strand": false,
"transcript": "ENST00000889106.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1148,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7092,
"cdna_start": 2990,
"cds_end": null,
"cds_length": 3447,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_031466.8",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_113654.5",
"strand": false,
"transcript": "NM_031466.8",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1148,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7092,
"cdna_start": 2990,
"cds_end": null,
"cds_length": 3447,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000648948.2",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000498020.1",
"strand": false,
"transcript": "ENST00000648948.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1148,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4356,
"cdna_start": 2873,
"cds_end": null,
"cds_length": 3447,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000889103.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559162.1",
"strand": false,
"transcript": "ENST00000889103.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1148,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4283,
"cdna_start": 2801,
"cds_end": null,
"cds_length": 3447,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000889105.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559164.1",
"strand": false,
"transcript": "ENST00000889105.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1148,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4265,
"cdna_start": 2782,
"cds_end": null,
"cds_length": 3447,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000889109.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559168.1",
"strand": false,
"transcript": "ENST00000889109.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1146,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4307,
"cdna_start": 2831,
"cds_end": null,
"cds_length": 3441,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000967712.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637771.1",
"strand": false,
"transcript": "ENST00000967712.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1139,
"aa_ref": "S",
"aa_start": 885,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6872,
"cdna_start": 2770,
"cds_end": null,
"cds_length": 3420,
"cds_start": 2654,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001321646.2",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2654G>A",
"hgvs_p": "p.Ser885Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308575.1",
"strand": false,
"transcript": "NM_001321646.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1137,
"aa_ref": "S",
"aa_start": 885,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5375,
"cdna_start": 2773,
"cds_end": null,
"cds_length": 3414,
"cds_start": 2654,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000920031.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2654G>A",
"hgvs_p": "p.Ser885Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590090.1",
"strand": false,
"transcript": "ENST00000920031.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1136,
"aa_ref": "S",
"aa_start": 882,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4223,
"cdna_start": 2743,
"cds_end": null,
"cds_length": 3411,
"cds_start": 2645,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000920035.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2645G>A",
"hgvs_p": "p.Ser882Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590094.1",
"strand": false,
"transcript": "ENST00000920035.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1111,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6788,
"cdna_start": 2797,
"cds_end": null,
"cds_length": 3336,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001374683.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001361612.1",
"strand": false,
"transcript": "NM_001374683.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1111,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4186,
"cdna_start": 2816,
"cds_end": null,
"cds_length": 3336,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000967713.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637772.1",
"strand": false,
"transcript": "ENST00000967713.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1105,
"aa_ref": "S",
"aa_start": 851,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4149,
"cdna_start": 2668,
"cds_end": null,
"cds_length": 3318,
"cds_start": 2552,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000889107.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2552G>A",
"hgvs_p": "p.Ser851Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559166.1",
"strand": false,
"transcript": "ENST00000889107.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1102,
"aa_ref": "S",
"aa_start": 885,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4138,
"cdna_start": 2767,
"cds_end": null,
"cds_length": 3309,
"cds_start": 2654,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000920033.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2654G>A",
"hgvs_p": "p.Ser885Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590092.1",
"strand": false,
"transcript": "ENST00000920033.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1100,
"aa_ref": "S",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6755,
"cdna_start": 2653,
"cds_end": null,
"cds_length": 3303,
"cds_start": 2537,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001374684.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2537G>A",
"hgvs_p": "p.Ser846Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001361613.1",
"strand": false,
"transcript": "NM_001374684.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1100,
"aa_ref": "S",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4150,
"cdna_start": 2653,
"cds_end": null,
"cds_length": 3303,
"cds_start": 2537,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000889102.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2537G>A",
"hgvs_p": "p.Ser846Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559161.1",
"strand": false,
"transcript": "ENST00000889102.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1096,
"aa_ref": "S",
"aa_start": 842,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4120,
"cdna_start": 2638,
"cds_end": null,
"cds_length": 3291,
"cds_start": 2525,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000889108.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2525G>A",
"hgvs_p": "p.Ser842Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559167.1",
"strand": false,
"transcript": "ENST00000889108.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1096,
"aa_ref": "S",
"aa_start": 842,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4259,
"cdna_start": 2777,
"cds_end": null,
"cds_length": 3291,
"cds_start": 2525,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000920032.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2525G>A",
"hgvs_p": "p.Ser842Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590091.1",
"strand": false,
"transcript": "ENST00000920032.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1088,
"aa_ref": "S",
"aa_start": 834,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4061,
"cdna_start": 2579,
"cds_end": null,
"cds_length": 3267,
"cds_start": 2501,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000920036.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2501G>A",
"hgvs_p": "p.Ser834Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590095.1",
"strand": false,
"transcript": "ENST00000920036.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1077,
"aa_ref": "S",
"aa_start": 823,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4069,
"cdna_start": 2587,
"cds_end": null,
"cds_length": 3234,
"cds_start": 2468,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000889104.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2468G>A",
"hgvs_p": "p.Ser823Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559163.1",
"strand": false,
"transcript": "ENST00000889104.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "S",
"aa_start": 814,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4034,
"cdna_start": 2551,
"cds_end": null,
"cds_length": 3207,
"cds_start": 2441,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000920034.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2441G>A",
"hgvs_p": "p.Ser814Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590093.1",
"strand": false,
"transcript": "ENST00000920034.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1068,
"aa_ref": "S",
"aa_start": 851,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4034,
"cdna_start": 2664,
"cds_end": null,
"cds_length": 3207,
"cds_start": 2552,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000967714.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2552G>A",
"hgvs_p": "p.Ser851Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637773.1",
"strand": false,
"transcript": "ENST00000967714.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1057,
"aa_ref": "S",
"aa_start": 803,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4199,
"cdna_start": 2717,
"cds_end": null,
"cds_length": 3174,
"cds_start": 2408,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000889101.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2408G>A",
"hgvs_p": "p.Ser803Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559160.1",
"strand": false,
"transcript": "ENST00000889101.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1237,
"aa_ref": "S",
"aa_start": 983,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7065,
"cdna_start": 2963,
"cds_end": null,
"cds_length": 3714,
"cds_start": 2948,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_011517326.3",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2948G>A",
"hgvs_p": "p.Ser983Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011515628.1",
"strand": false,
"transcript": "XM_011517326.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1128,
"aa_ref": "S",
"aa_start": 992,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4047,
"cdna_start": 2990,
"cds_end": null,
"cds_length": 3387,
"cds_start": 2975,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_011517328.3",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2975G>A",
"hgvs_p": "p.Ser992Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011515630.1",
"strand": false,
"transcript": "XM_011517328.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1119,
"aa_ref": "S",
"aa_start": 983,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4020,
"cdna_start": 2963,
"cds_end": null,
"cds_length": 3360,
"cds_start": 2948,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_047422294.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2948G>A",
"hgvs_p": "p.Ser983Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047278250.1",
"strand": false,
"transcript": "XM_047422294.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1041,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3478,
"cdna_start": 2797,
"cds_end": null,
"cds_length": 3126,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047422295.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047278251.1",
"strand": false,
"transcript": "XM_047422295.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1030,
"aa_ref": "S",
"aa_start": 894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3854,
"cdna_start": 2797,
"cds_end": null,
"cds_length": 3093,
"cds_start": 2681,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047422296.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2681G>A",
"hgvs_p": "p.Ser894Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047278252.1",
"strand": false,
"transcript": "XM_047422296.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1021,
"aa_ref": "S",
"aa_start": 885,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3827,
"cdna_start": 2770,
"cds_end": null,
"cds_length": 3066,
"cds_start": 2654,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_047422297.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.2654G>A",
"hgvs_p": "p.Ser885Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047278253.1",
"strand": false,
"transcript": "XM_047422297.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 688,
"aa_ref": "S",
"aa_start": 434,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5788,
"cdna_start": 1686,
"cds_end": null,
"cds_length": 2067,
"cds_start": 1301,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_017013894.3",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.1301G>A",
"hgvs_p": "p.Ser434Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016869383.1",
"strand": false,
"transcript": "XM_017013894.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 631,
"aa_ref": "S",
"aa_start": 377,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5456,
"cdna_start": 1354,
"cds_end": null,
"cds_length": 1896,
"cds_start": 1130,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011517330.3",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "c.1130G>A",
"hgvs_p": "p.Ser377Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011515632.1",
"strand": false,
"transcript": "XM_011517330.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 518,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000517667.5",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "n.403G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000517667.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 560,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000520532.5",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "n.528G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000520532.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 705,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000523777.5",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "n.290G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000523777.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1970,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000698172.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000289741",
"hgvs_c": "n.1739G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000698172.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 6945,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NR_164662.1",
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"hgvs_c": "n.2770G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_164662.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs34181302",
"effect": "missense_variant",
"frequency_reference_population": 0.000059478818,
"gene_hgnc_id": 30832,
"gene_symbol": "TRAPPC9",
"gnomad_exomes_ac": 59,
"gnomad_exomes_af": 0.000040362,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 37,
"gnomad_genomes_af": 0.000243021,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Inborn genetic diseases|Intellectual disability, autosomal recessive 13|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.592,
"pos": 140023955,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.223,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001374682.1"
}
]
}