← 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: 6-33451831-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=33451831&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 10,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SYNGAP1",
"hgnc_id": 11497,
"hgvs_c": "c.3957C>T",
"hgvs_p": "p.Ala1319Ala",
"inheritance_mode": "AD,Unknown",
"pathogenic_score": 0,
"score": -10,
"transcript": "NM_006772.3",
"verdict": "Benign"
},
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "SYNGAP1-AS1",
"hgnc_id": 53831,
"hgvs_c": "n.136+2439G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -4,
"transcript": "NR_174954.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_score": -10,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.56,
"chr": "6",
"clinvar_classification": "Likely benign",
"clinvar_disease": " autosomal dominant 5,Intellectual disability",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5600000023841858,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1343,
"aa_ref": "A",
"aa_start": 1319,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6015,
"cdna_start": 4157,
"cds_end": null,
"cds_length": 4032,
"cds_start": 3957,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_006772.3",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3957C>T",
"hgvs_p": "p.Ala1319Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000646630.1",
"protein_coding": true,
"protein_id": "NP_006763.2",
"strand": true,
"transcript": "NM_006772.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1343,
"aa_ref": "A",
"aa_start": 1319,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6015,
"cdna_start": 4157,
"cds_end": null,
"cds_length": 4032,
"cds_start": 3957,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000646630.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3957C>T",
"hgvs_p": "p.Ala1319Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006772.3",
"protein_coding": true,
"protein_id": "ENSP00000496007.1",
"strand": true,
"transcript": "ENST00000646630.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1308,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4051,
"cdna_start": null,
"cds_end": null,
"cds_length": 3927,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000644458.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*29C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495541.1",
"strand": true,
"transcript": "ENST00000644458.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1292,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3929,
"cdna_start": null,
"cds_end": null,
"cds_length": 3879,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000449372.7",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*29C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000416519.4",
"strand": true,
"transcript": "ENST00000449372.7",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5827,
"cdna_start": null,
"cds_end": null,
"cds_length": 3858,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000418600.7",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*111C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403636.3",
"strand": true,
"transcript": "ENST00000418600.7",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1249,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4040,
"cdna_start": null,
"cds_end": null,
"cds_length": 3750,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000645250.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*29C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000494861.1",
"strand": true,
"transcript": "ENST00000645250.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1343,
"aa_ref": "A",
"aa_start": 1319,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6010,
"cdna_start": 4152,
"cds_end": null,
"cds_length": 4032,
"cds_start": 3957,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000629380.3",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3957C>T",
"hgvs_p": "p.Ala1319Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000486463.1",
"strand": true,
"transcript": "ENST00000629380.3",
"transcript_support_level": 2
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1284,
"aa_ref": "A",
"aa_start": 1260,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4339,
"cdna_start": 3960,
"cds_end": null,
"cds_length": 3855,
"cds_start": 3780,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000428982.4",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3780C>T",
"hgvs_p": "p.Ala1260Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000412475.2",
"strand": true,
"transcript": "ENST00000428982.4",
"transcript_support_level": 5
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1257,
"aa_ref": "A",
"aa_start": 1233,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5604,
"cdna_start": 3746,
"cds_end": null,
"cds_length": 3774,
"cds_start": 3699,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000682587.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3699C>T",
"hgvs_p": "p.Ala1233Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000507403.1",
"strand": true,
"transcript": "ENST00000682587.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1344,
"aa_ref": "A",
"aa_start": 1320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6018,
"cdna_start": 4160,
"cds_end": null,
"cds_length": 4035,
"cds_start": 3960,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047419450.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3960C>T",
"hgvs_p": "p.Ala1320Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275406.1",
"strand": true,
"transcript": "XM_047419450.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1342,
"aa_ref": "A",
"aa_start": 1318,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6012,
"cdna_start": 4154,
"cds_end": null,
"cds_length": 4029,
"cds_start": 3954,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047419451.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3954C>T",
"hgvs_p": "p.Ala1318Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275407.1",
"strand": true,
"transcript": "XM_047419451.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1330,
"aa_ref": "A",
"aa_start": 1306,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5976,
"cdna_start": 4118,
"cds_end": null,
"cds_length": 3993,
"cds_start": 3918,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047419452.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3918C>T",
"hgvs_p": "p.Ala1306Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275408.1",
"strand": true,
"transcript": "XM_047419452.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1329,
"aa_ref": "A",
"aa_start": 1305,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5973,
"cdna_start": 4115,
"cds_end": null,
"cds_length": 3990,
"cds_start": 3915,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047419453.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3915C>T",
"hgvs_p": "p.Ala1305Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275409.1",
"strand": true,
"transcript": "XM_047419453.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1328,
"aa_ref": "A",
"aa_start": 1304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5970,
"cdna_start": 4112,
"cds_end": null,
"cds_length": 3987,
"cds_start": 3912,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047419454.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3912C>T",
"hgvs_p": "p.Ala1304Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275410.1",
"strand": true,
"transcript": "XM_047419454.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1316,
"aa_ref": "A",
"aa_start": 1292,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5967,
"cdna_start": 4109,
"cds_end": null,
"cds_length": 3951,
"cds_start": 3876,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047419455.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3876C>T",
"hgvs_p": "p.Ala1292Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275411.1",
"strand": true,
"transcript": "XM_047419455.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1316,
"aa_ref": "A",
"aa_start": 1292,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7647,
"cdna_start": 5789,
"cds_end": null,
"cds_length": 3951,
"cds_start": 3876,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047419456.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3876C>T",
"hgvs_p": "p.Ala1292Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275412.1",
"strand": true,
"transcript": "XM_047419456.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1304,
"aa_ref": "A",
"aa_start": 1280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5898,
"cdna_start": 4040,
"cds_end": null,
"cds_length": 3915,
"cds_start": 3840,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_047419457.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3840C>T",
"hgvs_p": "p.Ala1280Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275413.1",
"strand": true,
"transcript": "XM_047419457.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1285,
"aa_ref": "A",
"aa_start": 1261,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6326,
"cdna_start": 4468,
"cds_end": null,
"cds_length": 3858,
"cds_start": 3783,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_047419462.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3783C>T",
"hgvs_p": "p.Ala1261Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275418.1",
"strand": true,
"transcript": "XM_047419462.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1270,
"aa_ref": "A",
"aa_start": 1246,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6281,
"cdna_start": 4423,
"cds_end": null,
"cds_length": 3813,
"cds_start": 3738,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_047419466.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.3738C>T",
"hgvs_p": "p.Ala1246Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275422.1",
"strand": true,
"transcript": "XM_047419466.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1292,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5966,
"cdna_start": null,
"cds_end": null,
"cds_length": 3879,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001130066.2",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*29C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001123538.1",
"strand": true,
"transcript": "NM_001130066.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1292,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5966,
"cdna_start": null,
"cds_end": null,
"cds_length": 3879,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047419465.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*29C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275421.1",
"strand": true,
"transcript": "XM_047419465.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6028,
"cdna_start": null,
"cds_end": null,
"cds_length": 3858,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047419463.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*112C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275419.1",
"strand": true,
"transcript": "XM_047419463.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6031,
"cdna_start": null,
"cds_end": null,
"cds_length": 3858,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047419464.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*115C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275420.1",
"strand": true,
"transcript": "XM_047419464.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4556,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000293748.9",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "n.*137C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000293748.6",
"strand": true,
"transcript": "ENST00000293748.9",
"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": 161,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000636146.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "n.161C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000636146.1",
"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": 6095,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XR_007059351.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "n.4237C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007059351.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4556,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000293748.9",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "n.*137C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000293748.6",
"strand": true,
"transcript": "ENST00000293748.9",
"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": 1030,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000630418.2",
"gene_hgnc_id": 53831,
"gene_symbol": "SYNGAP1-AS1",
"hgvs_c": "n.184+2439G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000630418.2",
"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": 1275,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000815438.1",
"gene_hgnc_id": 53831,
"gene_symbol": "SYNGAP1-AS1",
"hgvs_c": "n.186+2439G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000815438.1",
"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": 800,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000815439.1",
"gene_hgnc_id": 53831,
"gene_symbol": "SYNGAP1-AS1",
"hgvs_c": "n.147+2439G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000815439.1",
"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": 448,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_174954.1",
"gene_hgnc_id": 53831,
"gene_symbol": "SYNGAP1-AS1",
"hgvs_c": "n.136+2439G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_174954.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1299,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6890,
"cdna_start": null,
"cds_end": null,
"cds_length": 3900,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047419458.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*3028C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275414.1",
"strand": true,
"transcript": "XM_047419458.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1297,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6884,
"cdna_start": null,
"cds_end": null,
"cds_length": 3894,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047419460.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*3028C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275416.1",
"strand": true,
"transcript": "XM_047419460.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6903,
"cdna_start": null,
"cds_end": null,
"cds_length": 3858,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047419461.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*3083C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275417.1",
"strand": true,
"transcript": "XM_047419461.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1245,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6728,
"cdna_start": null,
"cds_end": null,
"cds_length": 3738,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047419467.1",
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"hgvs_c": "c.*3028C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275423.1",
"strand": true,
"transcript": "XM_047419467.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs773538561",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0000044999006,
"gene_hgnc_id": 11497,
"gene_symbol": "SYNGAP1",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.00000355943,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000132564,
"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": "Likely benign",
"phenotype_combined": "Intellectual disability, autosomal dominant 5",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.615,
"pos": 33451831,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006772.3"
}
]
}