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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: 19-4362370-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=4362370&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 4362370,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003025.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.869G>A",
"hgvs_p": "p.Arg290Gln",
"transcript": "NM_003025.4",
"protein_id": "NP_003016.1",
"transcript_support_level": null,
"aa_start": 290,
"aa_end": null,
"aa_length": 368,
"cds_start": 869,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000269886.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003025.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.869G>A",
"hgvs_p": "p.Arg290Gln",
"transcript": "ENST00000269886.7",
"protein_id": "ENSP00000269886.2",
"transcript_support_level": 1,
"aa_start": 290,
"aa_end": null,
"aa_length": 368,
"cds_start": 869,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003025.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000269886.7"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.866G>A",
"hgvs_p": "p.Arg289Gln",
"transcript": "ENST00000908568.1",
"protein_id": "ENSP00000578627.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 367,
"cds_start": 866,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908568.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.830G>A",
"hgvs_p": "p.Arg277Gln",
"transcript": "ENST00000945946.1",
"protein_id": "ENSP00000616005.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 355,
"cds_start": 830,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945946.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.725G>A",
"hgvs_p": "p.Arg242Gln",
"transcript": "NM_001199943.2",
"protein_id": "NP_001186872.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 320,
"cds_start": 725,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199943.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.725G>A",
"hgvs_p": "p.Arg242Gln",
"transcript": "ENST00000417295.6",
"protein_id": "ENSP00000404568.2",
"transcript_support_level": 2,
"aa_start": 242,
"aa_end": null,
"aa_length": 320,
"cds_start": 725,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000417295.6"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.677G>A",
"hgvs_p": "p.Arg226Gln",
"transcript": "NM_001199944.2",
"protein_id": "NP_001186873.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 304,
"cds_start": 677,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199944.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.677G>A",
"hgvs_p": "p.Arg226Gln",
"transcript": "ENST00000598564.5",
"protein_id": "ENSP00000470792.1",
"transcript_support_level": 2,
"aa_start": 226,
"aa_end": null,
"aa_length": 304,
"cds_start": 677,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000598564.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.674G>A",
"hgvs_p": "p.Arg225Gln",
"transcript": "ENST00000936273.1",
"protein_id": "ENSP00000606332.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 303,
"cds_start": 674,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936273.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.416G>A",
"hgvs_p": "p.Arg139Gln",
"transcript": "ENST00000908569.1",
"protein_id": "ENSP00000578628.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 217,
"cds_start": 416,
"cds_end": null,
"cds_length": 654,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908569.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280Gln",
"transcript": "XM_017027146.2",
"protein_id": "XP_016882635.1",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 358,
"cds_start": 839,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027146.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"hgvs_c": "c.764G>A",
"hgvs_p": "p.Arg255Gln",
"transcript": "XM_047439222.1",
"protein_id": "XP_047295178.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 333,
"cds_start": 764,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439222.1"
}
],
"gene_symbol": "SH3GL1",
"gene_hgnc_id": 10830,
"dbsnp": "rs997768573",
"frequency_reference_population": 0.000029159259,
"hom_count_reference_population": 0,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.0000267197,
"gnomad_genomes_af": 0.0000525479,
"gnomad_exomes_ac": 39,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1721593141555786,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.051,
"revel_prediction": "Benign",
"alphamissense_score": 0.0915,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.091,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003025.4",
"gene_symbol": "SH3GL1",
"hgnc_id": 10830,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.869G>A",
"hgvs_p": "p.Arg290Gln"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}