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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: 2-149582194-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=149582194&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 149582194,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_015702.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "NM_015702.3",
"protein_id": "NP_056517.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 296,
"cds_start": 87,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000303319.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015702.3"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000303319.10",
"protein_id": "ENSP00000301920.5",
"transcript_support_level": 1,
"aa_start": 29,
"aa_end": null,
"aa_length": 296,
"cds_start": 87,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015702.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000303319.10"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000934249.1",
"protein_id": "ENSP00000604308.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 337,
"cds_start": 87,
"cds_end": null,
"cds_length": 1014,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934249.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000422782.2",
"protein_id": "ENSP00000408331.2",
"transcript_support_level": 5,
"aa_start": 29,
"aa_end": null,
"aa_length": 330,
"cds_start": 87,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000422782.2"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000428879.5",
"protein_id": "ENSP00000389060.1",
"transcript_support_level": 2,
"aa_start": 29,
"aa_end": null,
"aa_length": 296,
"cds_start": 87,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428879.5"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000893992.1",
"protein_id": "ENSP00000564051.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 296,
"cds_start": 87,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893992.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000893995.1",
"protein_id": "ENSP00000564054.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 296,
"cds_start": 87,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893995.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000893996.1",
"protein_id": "ENSP00000564055.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 296,
"cds_start": 87,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893996.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000893997.1",
"protein_id": "ENSP00000564056.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 296,
"cds_start": 87,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893997.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000949352.1",
"protein_id": "ENSP00000619411.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 296,
"cds_start": 87,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949352.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000934248.1",
"protein_id": "ENSP00000604307.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 289,
"cds_start": 87,
"cds_end": null,
"cds_length": 870,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934248.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000934250.1",
"protein_id": "ENSP00000604309.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 279,
"cds_start": 87,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934250.1"
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn",
"transcript": "ENST00000893994.1",
"protein_id": "ENSP00000564053.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 267,
"cds_start": 87,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893994.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"hgvs_c": "c.9+4895A>C",
"hgvs_p": null,
"transcript": "ENST00000893993.1",
"protein_id": "ENSP00000564052.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 96,
"cds_start": null,
"cds_end": null,
"cds_length": 291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893993.1"
}
],
"gene_symbol": "MMADHC",
"gene_hgnc_id": 25221,
"dbsnp": "rs61750442",
"frequency_reference_population": 0.009404678,
"hom_count_reference_population": 94,
"allele_count_reference_population": 15179,
"gnomad_exomes_af": 0.00961446,
"gnomad_genomes_af": 0.00739175,
"gnomad_exomes_ac": 14053,
"gnomad_genomes_ac": 1126,
"gnomad_exomes_homalt": 89,
"gnomad_genomes_homalt": 5,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.010101467370986938,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1599999964237213,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.327,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5332,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.253,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.16,
"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_015702.3",
"gene_symbol": "MMADHC",
"hgnc_id": 25221,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.87A>C",
"hgvs_p": "p.Lys29Asn"
}
],
"clinvar_disease": "Disorders of Intracellular Cobalamin Metabolism,Methylmalonic aciduria and homocystinuria type cblD,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:5",
"phenotype_combined": "Disorders of Intracellular Cobalamin Metabolism|not specified|not provided|Methylmalonic aciduria and homocystinuria type cblD",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}