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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: X-13776249-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=13776249&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GPM6B",
"hgnc_id": 4461,
"hgvs_c": "c.826G>A",
"hgvs_p": "p.Val276Ile",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001001995.3",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "OFD1",
"hgnc_id": 2567,
"hgvs_c": "n.3504C>T",
"hgvs_p": null,
"inheritance_mode": "XL,AD,AR",
"pathogenic_score": 0,
"score": -6,
"transcript": "ENST00000683454.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 79,
"alphamissense_prediction": null,
"alphamissense_score": 0.1567,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.12,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.17223888635635376,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 328,
"aa_ref": "V",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3118,
"cdna_start": 1015,
"cds_end": null,
"cds_length": 987,
"cds_start": 826,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001001995.3",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.826G>A",
"hgvs_p": "p.Val276Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000316715.9",
"protein_coding": true,
"protein_id": "NP_001001995.1",
"strand": false,
"transcript": "NM_001001995.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 328,
"aa_ref": "V",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3118,
"cdna_start": 1015,
"cds_end": null,
"cds_length": 987,
"cds_start": 826,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000316715.9",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.826G>A",
"hgvs_p": "p.Val276Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001001995.3",
"protein_coding": true,
"protein_id": "ENSP00000316861.4",
"strand": false,
"transcript": "ENST00000316715.9",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 305,
"aa_ref": "V",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1673,
"cdna_start": 991,
"cds_end": null,
"cds_length": 918,
"cds_start": 826,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000355135.6",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.826G>A",
"hgvs_p": "p.Val276Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000347258.2",
"strand": false,
"transcript": "ENST00000355135.6",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 265,
"aa_ref": "V",
"aa_start": 236,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1830,
"cdna_start": 1148,
"cds_end": null,
"cds_length": 798,
"cds_start": 706,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000356942.9",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.706G>A",
"hgvs_p": "p.Val236Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000349420.5",
"strand": false,
"transcript": "ENST00000356942.9",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 246,
"aa_ref": "V",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4474,
"cdna_start": 777,
"cds_end": null,
"cds_length": 741,
"cds_start": 649,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000454189.7",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.649G>A",
"hgvs_p": "p.Val217Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000389915.2",
"strand": false,
"transcript": "ENST00000454189.7",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 305,
"aa_ref": "V",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4712,
"cdna_start": 1015,
"cds_end": null,
"cds_length": 918,
"cds_start": 826,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001001996.3",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.826G>A",
"hgvs_p": "p.Val276Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001001996.1",
"strand": false,
"transcript": "NM_001001996.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 302,
"aa_ref": "V",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1372,
"cdna_start": 1029,
"cds_end": null,
"cds_length": 909,
"cds_start": 748,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000493677.5",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.748G>A",
"hgvs_p": "p.Val250Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419904.1",
"strand": false,
"transcript": "ENST00000493677.5",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 269,
"aa_ref": "V",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2880,
"cdna_start": 777,
"cds_end": null,
"cds_length": 810,
"cds_start": 649,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001318729.2",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.649G>A",
"hgvs_p": "p.Val217Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305658.1",
"strand": false,
"transcript": "NM_001318729.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 265,
"aa_ref": "V",
"aa_start": 236,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4592,
"cdna_start": 895,
"cds_end": null,
"cds_length": 798,
"cds_start": 706,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_005278.5",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.706G>A",
"hgvs_p": "p.Val236Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_005269.1",
"strand": false,
"transcript": "NM_005278.5",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 246,
"aa_ref": "V",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4474,
"cdna_start": 777,
"cds_end": null,
"cds_length": 741,
"cds_start": 649,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001001994.3",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.649G>A",
"hgvs_p": "p.Val217Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001001994.1",
"strand": false,
"transcript": "NM_001001994.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 179,
"aa_ref": "V",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1033,
"cdna_start": 734,
"cds_end": null,
"cds_length": 540,
"cds_start": 448,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000398361.7",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.448G>A",
"hgvs_p": "p.Val150Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000381402.3",
"strand": false,
"transcript": "ENST00000398361.7",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 309,
"aa_ref": "V",
"aa_start": 257,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3000,
"cdna_start": 897,
"cds_end": null,
"cds_length": 930,
"cds_start": 769,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011545497.3",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.769G>A",
"hgvs_p": "p.Val257Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011543799.1",
"strand": false,
"transcript": "XM_011545497.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 302,
"aa_ref": "V",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 19769,
"cdna_start": 17666,
"cds_end": null,
"cds_length": 909,
"cds_start": 748,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047442007.1",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.748G>A",
"hgvs_p": "p.Val250Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047297963.1",
"strand": false,
"transcript": "XM_047442007.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 288,
"aa_ref": "V",
"aa_start": 236,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2998,
"cdna_start": 895,
"cds_end": null,
"cds_length": 867,
"cds_start": 706,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_005274489.6",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.706G>A",
"hgvs_p": "p.Val236Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005274546.1",
"strand": false,
"transcript": "XM_005274489.6",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 286,
"aa_ref": "V",
"aa_start": 257,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4594,
"cdna_start": 897,
"cds_end": null,
"cds_length": 861,
"cds_start": 769,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_017029432.2",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.769G>A",
"hgvs_p": "p.Val257Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884921.1",
"strand": false,
"transcript": "XM_017029432.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 202,
"aa_ref": "V",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3816,
"cdna_start": 1713,
"cds_end": null,
"cds_length": 609,
"cds_start": 448,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047442009.1",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "c.448G>A",
"hgvs_p": "p.Val150Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047297965.1",
"strand": false,
"transcript": "XM_047442009.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 580,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000472735.5",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "n.392G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000472735.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 683,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000495211.2",
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"hgvs_c": "n.601G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000495211.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5210,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000683454.1",
"gene_hgnc_id": 2567,
"gene_symbol": "OFD1",
"hgvs_c": "n.3504C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000683454.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs757587714",
"effect": "missense_variant",
"frequency_reference_population": 0.00006549212,
"gene_hgnc_id": 4461,
"gene_symbol": "GPM6B",
"gnomad_exomes_ac": 57,
"gnomad_exomes_af": 0.000052086,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 22,
"gnomad_genomes_af": 0.000196588,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 14,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.632,
"pos": 13776249,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.642,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001001995.3"
}
]
}