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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: 17-74749174-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=74749174&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 74749174,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_004252.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val",
"transcript": "NM_004252.5",
"protein_id": "NP_004243.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 358,
"cds_start": 328,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000262613.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004252.5"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val",
"transcript": "ENST00000262613.10",
"protein_id": "ENSP00000262613.5",
"transcript_support_level": 1,
"aa_start": 110,
"aa_end": null,
"aa_length": 358,
"cds_start": 328,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004252.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262613.10"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val",
"transcript": "ENST00000851804.1",
"protein_id": "ENSP00000521863.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 417,
"cds_start": 328,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851804.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val",
"transcript": "ENST00000851803.1",
"protein_id": "ENSP00000521862.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 361,
"cds_start": 328,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851803.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val",
"transcript": "ENST00000851800.1",
"protein_id": "ENSP00000521859.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 357,
"cds_start": 328,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851800.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val",
"transcript": "ENST00000967136.1",
"protein_id": "ENSP00000637195.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 347,
"cds_start": 328,
"cds_end": null,
"cds_length": 1044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967136.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val",
"transcript": "ENST00000851801.1",
"protein_id": "ENSP00000521860.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 304,
"cds_start": 328,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851801.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val",
"transcript": "ENST00000851802.1",
"protein_id": "ENSP00000521861.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 292,
"cds_start": 328,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851802.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val",
"transcript": "ENST00000583369.5",
"protein_id": "ENSP00000464321.1",
"transcript_support_level": 3,
"aa_start": 110,
"aa_end": null,
"aa_length": 214,
"cds_start": 328,
"cds_end": null,
"cds_length": 646,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000583369.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9A3R1-AS1",
"gene_hgnc_id": 55322,
"hgvs_c": "n.694G>C",
"hgvs_p": null,
"transcript": "NR_187307.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_187307.1"
}
],
"gene_symbol": "NHERF1",
"gene_hgnc_id": 11075,
"dbsnp": "rs35910969",
"frequency_reference_population": 0.025296938,
"hom_count_reference_population": 619,
"allele_count_reference_population": 38801,
"gnomad_exomes_af": 0.0263022,
"gnomad_genomes_af": 0.0161685,
"gnomad_exomes_ac": 36341,
"gnomad_genomes_ac": 2460,
"gnomad_exomes_homalt": 586,
"gnomad_genomes_homalt": 33,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003754734992980957,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.07,
"revel_prediction": "Benign",
"alphamissense_score": 0.0954,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.095,
"phylop100way_prediction": "Benign",
"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": -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_004252.5",
"gene_symbol": "NHERF1",
"hgnc_id": 11075,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.328C>G",
"hgvs_p": "p.Leu110Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NR_187307.1",
"gene_symbol": "SLC9A3R1-AS1",
"hgnc_id": 55322,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.694G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Hypophosphatemic nephrolithiasis/osteoporosis 2,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "Hypophosphatemic nephrolithiasis/osteoporosis 2|not provided|not specified",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}