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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: 3-46902569-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=46902569&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 46902569,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000449590.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"transcript": "NM_000316.3",
"protein_id": "NP_000307.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 593,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1483,
"cdna_end": null,
"cdna_length": 2153,
"mane_select": "ENST00000449590.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"transcript": "ENST00000449590.6",
"protein_id": "ENSP00000402723.1",
"transcript_support_level": 1,
"aa_start": 419,
"aa_end": null,
"aa_length": 593,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1483,
"cdna_end": null,
"cdna_length": 2153,
"mane_select": "NM_000316.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"transcript": "ENST00000313049.9",
"protein_id": "ENSP00000321999.4",
"transcript_support_level": 1,
"aa_start": 419,
"aa_end": null,
"aa_length": 593,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1458,
"cdna_end": null,
"cdna_length": 2123,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"transcript": "ENST00000430002.6",
"protein_id": "ENSP00000413774.2",
"transcript_support_level": 1,
"aa_start": 419,
"aa_end": null,
"aa_length": 593,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1321,
"cdna_end": null,
"cdna_length": 1947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"transcript": "NM_001184744.1",
"protein_id": "NP_001171673.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 593,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1321,
"cdna_end": null,
"cdna_length": 1991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"transcript": "ENST00000418619.5",
"protein_id": "ENSP00000411424.1",
"transcript_support_level": 5,
"aa_start": 419,
"aa_end": null,
"aa_length": 593,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1404,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile",
"transcript": "ENST00000427125.6",
"protein_id": "ENSP00000400977.2",
"transcript_support_level": 5,
"aa_start": 419,
"aa_end": null,
"aa_length": 526,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 1588,
"cdna_end": null,
"cdna_length": 1914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1294G>A",
"hgvs_p": "p.Val432Ile",
"transcript": "XM_011533967.4",
"protein_id": "XP_011532269.1",
"transcript_support_level": null,
"aa_start": 432,
"aa_end": null,
"aa_length": 606,
"cds_start": 1294,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 1522,
"cdna_end": null,
"cdna_length": 2192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1294G>A",
"hgvs_p": "p.Val432Ile",
"transcript": "XM_017006932.3",
"protein_id": "XP_016862421.1",
"transcript_support_level": null,
"aa_start": 432,
"aa_end": null,
"aa_length": 606,
"cds_start": 1294,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 1550,
"cdna_end": null,
"cdna_length": 2220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1294G>A",
"hgvs_p": "p.Val432Ile",
"transcript": "XM_047448632.1",
"protein_id": "XP_047304588.1",
"transcript_support_level": null,
"aa_start": 432,
"aa_end": null,
"aa_length": 606,
"cds_start": 1294,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 2102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1276G>A",
"hgvs_p": "p.Val426Ile",
"transcript": "XM_011533968.3",
"protein_id": "XP_011532270.1",
"transcript_support_level": null,
"aa_start": 426,
"aa_end": null,
"aa_length": 600,
"cds_start": 1276,
"cds_end": null,
"cds_length": 1803,
"cdna_start": 1399,
"cdna_end": null,
"cdna_length": 2069,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1290G>A",
"hgvs_p": "p.Ala430Ala",
"transcript": "XM_017006934.2",
"protein_id": "XP_016862423.1",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 516,
"cds_start": 1290,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 1518,
"cdna_end": null,
"cdna_length": 2188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.1251G>A",
"hgvs_p": "p.Ala417Ala",
"transcript": "XM_047448633.1",
"protein_id": "XP_047304589.1",
"transcript_support_level": null,
"aa_start": 417,
"aa_end": null,
"aa_length": 503,
"cds_start": 1251,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 1479,
"cdna_end": null,
"cdna_length": 2149,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "n.*192G>A",
"hgvs_p": null,
"transcript": "ENST00000428220.1",
"protein_id": "ENSP00000389811.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "n.*192G>A",
"hgvs_p": null,
"transcript": "ENST00000428220.1",
"protein_id": "ENSP00000389811.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.-30G>A",
"hgvs_p": null,
"transcript": "ENST00000422115.2",
"protein_id": "ENSP00000396176.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 182,
"cds_start": -4,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"dbsnp": "rs758673796",
"frequency_reference_population": 0.000019215178,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000157418,
"gnomad_genomes_af": 0.0000525521,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.40134289860725403,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.236,
"revel_prediction": "Benign",
"alphamissense_score": 0.122,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.148,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS1_Supporting",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000449590.6",
"gene_symbol": "PTH1R",
"hgnc_id": 9608,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1255G>A",
"hgvs_p": "p.Val419Ile"
}
],
"clinvar_disease": " Jansen type,Chondrodysplasia Blomstrand type,Inborn genetic diseases,Metaphyseal chondrodysplasia,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 B:1",
"phenotype_combined": "Metaphyseal chondrodysplasia, Jansen type|Chondrodysplasia Blomstrand type|not provided|Inborn genetic diseases|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}