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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: 4-672512-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=672512&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 672512,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_007100.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "c.198C>A",
"hgvs_p": "p.Ser66Arg",
"transcript": "NM_007100.4",
"protein_id": "NP_009031.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 69,
"cds_start": 198,
"cds_end": null,
"cds_length": 210,
"cdna_start": 227,
"cdna_end": null,
"cdna_length": 303,
"mane_select": "ENST00000304312.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007100.4"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "c.198C>A",
"hgvs_p": "p.Ser66Arg",
"transcript": "ENST00000304312.5",
"protein_id": "ENSP00000306003.4",
"transcript_support_level": 1,
"aa_start": 66,
"aa_end": null,
"aa_length": 69,
"cds_start": 198,
"cds_end": null,
"cds_length": 210,
"cdna_start": 227,
"cdna_end": null,
"cdna_length": 303,
"mane_select": "NM_007100.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000304312.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "n.422C>A",
"hgvs_p": null,
"transcript": "ENST00000506525.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 496,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000506525.5"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "c.258C>A",
"hgvs_p": "p.Ser86Arg",
"transcript": "ENST00000932115.1",
"protein_id": "ENSP00000602174.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 89,
"cds_start": 258,
"cds_end": null,
"cds_length": 270,
"cdna_start": 380,
"cdna_end": null,
"cdna_length": 456,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932115.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "c.246C>A",
"hgvs_p": "p.Ser82Arg",
"transcript": "ENST00000895154.1",
"protein_id": "ENSP00000565213.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 85,
"cds_start": 246,
"cds_end": null,
"cds_length": 258,
"cdna_start": 267,
"cdna_end": null,
"cdna_length": 340,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000895154.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "c.237C>A",
"hgvs_p": "p.Ser79Arg",
"transcript": "ENST00000932118.1",
"protein_id": "ENSP00000602177.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 82,
"cds_start": 237,
"cds_end": null,
"cds_length": 249,
"cdna_start": 305,
"cdna_end": null,
"cdna_length": 381,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932118.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "c.198C>A",
"hgvs_p": "p.Ser66Arg",
"transcript": "ENST00000932116.1",
"protein_id": "ENSP00000602175.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 69,
"cds_start": 198,
"cds_end": null,
"cds_length": 210,
"cdna_start": 305,
"cdna_end": null,
"cdna_length": 394,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932116.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "c.180C>A",
"hgvs_p": "p.Ser60Arg",
"transcript": "ENST00000932117.1",
"protein_id": "ENSP00000602176.1",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 63,
"cds_start": 180,
"cds_end": null,
"cds_length": 192,
"cdna_start": 271,
"cdna_end": null,
"cdna_length": 347,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932117.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "n.226C>A",
"hgvs_p": null,
"transcript": "ENST00000505852.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 300,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000505852.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "n.229C>A",
"hgvs_p": null,
"transcript": "ENST00000515116.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 247,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000515116.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "n.317C>A",
"hgvs_p": null,
"transcript": "ENST00000515202.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 393,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000515202.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"hgvs_c": "n.172C>A",
"hgvs_p": null,
"transcript": "NR_033743.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 248,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033743.2"
}
],
"gene_symbol": "ATP5ME",
"gene_hgnc_id": 846,
"dbsnp": "rs1444328433",
"frequency_reference_population": 0.0000027364235,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273642,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20766347646713257,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.096,
"revel_prediction": "Benign",
"alphamissense_score": 0.8017,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.371,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 2,
"pathogenic_score": 4,
"criteria": [
"PM1",
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_007100.4",
"gene_symbol": "ATP5ME",
"hgnc_id": 846,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.198C>A",
"hgvs_p": "p.Ser66Arg"
}
],
"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
}