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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: 1-116584795-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=116584795&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 116584795,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001542.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2698G>A",
"hgvs_p": "p.Val900Met",
"transcript": "NM_001007237.3",
"protein_id": "NP_001007238.1",
"transcript_support_level": null,
"aa_start": 900,
"aa_end": null,
"aa_length": 1194,
"cds_start": 2698,
"cds_end": null,
"cds_length": 3585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000369486.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001007237.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2698G>A",
"hgvs_p": "p.Val900Met",
"transcript": "ENST00000369486.8",
"protein_id": "ENSP00000358498.4",
"transcript_support_level": 1,
"aa_start": 900,
"aa_end": null,
"aa_length": 1194,
"cds_start": 2698,
"cds_end": null,
"cds_length": 3585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001007237.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369486.8"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2758G>A",
"hgvs_p": "p.Val920Met",
"transcript": "NM_001542.4",
"protein_id": "NP_001533.2",
"transcript_support_level": null,
"aa_start": 920,
"aa_end": null,
"aa_length": 1214,
"cds_start": 2758,
"cds_end": null,
"cds_length": 3645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001542.4"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2758G>A",
"hgvs_p": "p.Val920Met",
"transcript": "ENST00000318837.6",
"protein_id": "ENSP00000321184.6",
"transcript_support_level": 2,
"aa_start": 920,
"aa_end": null,
"aa_length": 1214,
"cds_start": 2758,
"cds_end": null,
"cds_length": 3645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000318837.6"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2758G>A",
"hgvs_p": "p.Val920Met",
"transcript": "ENST00000369483.5",
"protein_id": "ENSP00000358495.1",
"transcript_support_level": 5,
"aa_start": 920,
"aa_end": null,
"aa_length": 1214,
"cds_start": 2758,
"cds_end": null,
"cds_length": 3645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369483.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2755G>A",
"hgvs_p": "p.Val919Met",
"transcript": "ENST00000897088.1",
"protein_id": "ENSP00000567147.1",
"transcript_support_level": null,
"aa_start": 919,
"aa_end": null,
"aa_length": 1213,
"cds_start": 2755,
"cds_end": null,
"cds_length": 3642,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897088.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2698G>A",
"hgvs_p": "p.Val900Met",
"transcript": "ENST00000897089.1",
"protein_id": "ENSP00000567148.1",
"transcript_support_level": null,
"aa_start": 900,
"aa_end": null,
"aa_length": 1194,
"cds_start": 2698,
"cds_end": null,
"cds_length": 3585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897089.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2590G>A",
"hgvs_p": "p.Val864Met",
"transcript": "ENST00000897090.1",
"protein_id": "ENSP00000567149.1",
"transcript_support_level": null,
"aa_start": 864,
"aa_end": null,
"aa_length": 1158,
"cds_start": 2590,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897090.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2773G>A",
"hgvs_p": "p.Val925Met",
"transcript": "XM_006710593.4",
"protein_id": "XP_006710656.1",
"transcript_support_level": null,
"aa_start": 925,
"aa_end": null,
"aa_length": 1219,
"cds_start": 2773,
"cds_end": null,
"cds_length": 3660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006710593.4"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2758G>A",
"hgvs_p": "p.Val920Met",
"transcript": "XM_011541315.2",
"protein_id": "XP_011539617.1",
"transcript_support_level": null,
"aa_start": 920,
"aa_end": null,
"aa_length": 1214,
"cds_start": 2758,
"cds_end": null,
"cds_length": 3645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541315.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2755G>A",
"hgvs_p": "p.Val919Met",
"transcript": "XM_047419042.1",
"protein_id": "XP_047274998.1",
"transcript_support_level": null,
"aa_start": 919,
"aa_end": null,
"aa_length": 1213,
"cds_start": 2755,
"cds_end": null,
"cds_length": 3642,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419042.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2755G>A",
"hgvs_p": "p.Val919Met",
"transcript": "XM_047419052.1",
"protein_id": "XP_047275008.1",
"transcript_support_level": null,
"aa_start": 919,
"aa_end": null,
"aa_length": 1213,
"cds_start": 2755,
"cds_end": null,
"cds_length": 3642,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419052.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2713G>A",
"hgvs_p": "p.Val905Met",
"transcript": "XM_005270794.5",
"protein_id": "XP_005270851.1",
"transcript_support_level": null,
"aa_start": 905,
"aa_end": null,
"aa_length": 1199,
"cds_start": 2713,
"cds_end": null,
"cds_length": 3600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005270794.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.2698G>A",
"hgvs_p": "p.Val900Met",
"transcript": "XM_047419070.1",
"protein_id": "XP_047275026.1",
"transcript_support_level": null,
"aa_start": 900,
"aa_end": null,
"aa_length": 1194,
"cds_start": 2698,
"cds_end": null,
"cds_length": 3585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419070.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"hgvs_c": "c.1087G>A",
"hgvs_p": "p.Val363Met",
"transcript": "XM_011541316.3",
"protein_id": "XP_011539618.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 657,
"cds_start": 1087,
"cds_end": null,
"cds_length": 1974,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541316.3"
}
],
"gene_symbol": "IGSF3",
"gene_hgnc_id": 5950,
"dbsnp": "rs41301291",
"frequency_reference_population": 0.015385683,
"hom_count_reference_population": 267,
"allele_count_reference_population": 24836,
"gnomad_exomes_af": 0.0155609,
"gnomad_genomes_af": 0.0137046,
"gnomad_exomes_ac": 22748,
"gnomad_genomes_ac": 2088,
"gnomad_exomes_homalt": 238,
"gnomad_genomes_homalt": 29,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006508767604827881,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.211,
"revel_prediction": "Benign",
"alphamissense_score": 0.1009,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.782,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001542.4",
"gene_symbol": "IGSF3",
"hgnc_id": 5950,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.2758G>A",
"hgvs_p": "p.Val920Met"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}