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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: 3-136151262-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=136151262&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 136151262,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018133.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Ser540Asn",
"transcript": "NM_018133.4",
"protein_id": "NP_060603.2",
"transcript_support_level": null,
"aa_start": 540,
"aa_end": null,
"aa_length": 577,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1734,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000309993.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018133.4"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Ser540Asn",
"transcript": "ENST00000309993.3",
"protein_id": "ENSP00000311827.2",
"transcript_support_level": 1,
"aa_start": 540,
"aa_end": null,
"aa_length": 577,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1734,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018133.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000309993.3"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1607G>A",
"hgvs_p": "p.Ser536Asn",
"transcript": "ENST00000703105.1",
"protein_id": "ENSP00000515172.1",
"transcript_support_level": null,
"aa_start": 536,
"aa_end": null,
"aa_length": 573,
"cds_start": 1607,
"cds_end": null,
"cds_length": 1722,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000703105.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Ser466Asn",
"transcript": "NM_001145417.2",
"protein_id": "NP_001138889.1",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 503,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145417.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Ser466Asn",
"transcript": "ENST00000434835.2",
"protein_id": "ENSP00000387948.2",
"transcript_support_level": 2,
"aa_start": 466,
"aa_end": null,
"aa_length": 503,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000434835.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Ser466Asn",
"transcript": "ENST00000473093.2",
"protein_id": "ENSP00000418655.2",
"transcript_support_level": 4,
"aa_start": 466,
"aa_end": null,
"aa_length": 503,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000473093.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Ser466Asn",
"transcript": "ENST00000481989.2",
"protein_id": "ENSP00000418752.2",
"transcript_support_level": 4,
"aa_start": 466,
"aa_end": null,
"aa_length": 503,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000481989.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Ser466Asn",
"transcript": "ENST00000491050.2",
"protein_id": "ENSP00000417956.2",
"transcript_support_level": 4,
"aa_start": 466,
"aa_end": null,
"aa_length": 503,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000491050.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Ser466Asn",
"transcript": "ENST00000703103.1",
"protein_id": "ENSP00000515170.1",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 503,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000703103.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Ser466Asn",
"transcript": "ENST00000703104.1",
"protein_id": "ENSP00000515171.1",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 503,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000703104.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Ser466Asn",
"transcript": "XM_005247571.4",
"protein_id": "XP_005247628.1",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 503,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247571.4"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Ser466Asn",
"transcript": "XM_011512949.3",
"protein_id": "XP_011511251.1",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 503,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512949.3"
}
],
"gene_symbol": "MSL2",
"gene_hgnc_id": 25544,
"dbsnp": "rs137871177",
"frequency_reference_population": 0.0075763864,
"hom_count_reference_population": 68,
"allele_count_reference_population": 12230,
"gnomad_exomes_af": 0.00770783,
"gnomad_genomes_af": 0.00631499,
"gnomad_exomes_ac": 11268,
"gnomad_genomes_ac": 962,
"gnomad_exomes_homalt": 61,
"gnomad_genomes_homalt": 7,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005224466323852539,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.091,
"revel_prediction": "Benign",
"alphamissense_score": 0.2434,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.178,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_018133.4",
"gene_symbol": "MSL2",
"hgnc_id": 25544,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Ser540Asn"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}