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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: 4-55396241-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=55396241&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 55396241,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_018475.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "M",
"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": "TMEM165",
"gene_hgnc_id": 30760,
"hgvs_c": "c.52C>A",
"hgvs_p": "p.Leu18Met",
"transcript": "NM_018475.5",
"protein_id": "NP_060945.2",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 324,
"cds_start": 52,
"cds_end": null,
"cds_length": 975,
"cdna_start": 285,
"cdna_end": null,
"cdna_length": 1931,
"mane_select": "ENST00000381334.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"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": "TMEM165",
"gene_hgnc_id": 30760,
"hgvs_c": "c.52C>A",
"hgvs_p": "p.Leu18Met",
"transcript": "ENST00000381334.10",
"protein_id": "ENSP00000370736.5",
"transcript_support_level": 1,
"aa_start": 18,
"aa_end": null,
"aa_length": 324,
"cds_start": 52,
"cds_end": null,
"cds_length": 975,
"cdna_start": 285,
"cdna_end": null,
"cdna_length": 1931,
"mane_select": "NM_018475.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM165",
"gene_hgnc_id": 30760,
"hgvs_c": "c.-394C>A",
"hgvs_p": null,
"transcript": "XM_017008412.2",
"protein_id": "XP_016863901.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 261,
"cds_start": -4,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"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": "TMEM165",
"gene_hgnc_id": 30760,
"hgvs_c": "c.52C>A",
"hgvs_p": "p.Leu18Met",
"transcript": "ENST00000506198.5",
"protein_id": "ENSP00000425449.1",
"transcript_support_level": 2,
"aa_start": 18,
"aa_end": null,
"aa_length": 129,
"cds_start": 52,
"cds_end": null,
"cds_length": 390,
"cdna_start": 285,
"cdna_end": null,
"cdna_length": 828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"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": "TMEM165",
"gene_hgnc_id": 30760,
"hgvs_c": "c.52C>A",
"hgvs_p": "p.Leu18Met",
"transcript": "XM_011534394.4",
"protein_id": "XP_011532696.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 321,
"cds_start": 52,
"cds_end": null,
"cds_length": 966,
"cdna_start": 285,
"cdna_end": null,
"cdna_length": 2290,
"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": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM165",
"gene_hgnc_id": 30760,
"hgvs_c": "n.52C>A",
"hgvs_p": null,
"transcript": "ENST00000508404.5",
"protein_id": "ENSP00000422639.1",
"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": 1657,
"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": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM165",
"gene_hgnc_id": 30760,
"hgvs_c": "n.285C>A",
"hgvs_p": null,
"transcript": "NR_073070.2",
"protein_id": null,
"transcript_support_level": null,
"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": 2034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM165",
"gene_hgnc_id": 30760,
"hgvs_c": "c.-394C>A",
"hgvs_p": null,
"transcript": "XM_017008412.2",
"protein_id": "XP_016863901.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 261,
"cds_start": -4,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM165",
"gene_hgnc_id": 30760,
"hgvs_c": "n.-10C>A",
"hgvs_p": null,
"transcript": "ENST00000514070.1",
"protein_id": null,
"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": 433,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3-AS1",
"gene_hgnc_id": 44138,
"hgvs_c": "n.-145G>T",
"hgvs_p": null,
"transcript": "ENST00000819837.1",
"protein_id": null,
"transcript_support_level": null,
"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": 599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMEM165",
"gene_hgnc_id": 30760,
"dbsnp": "rs756276628",
"frequency_reference_population": 0.00024321862,
"hom_count_reference_population": 0,
"allele_count_reference_population": 364,
"gnomad_exomes_af": 0.000242465,
"gnomad_genomes_af": 0.000249878,
"gnomad_exomes_ac": 326,
"gnomad_genomes_ac": 38,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09977155923843384,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.1,
"revel_prediction": "Benign",
"alphamissense_score": 0.1765,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.409,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP2,BP4_Moderate",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 2,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_018475.5",
"gene_symbol": "TMEM165",
"hgnc_id": 30760,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.52C>A",
"hgvs_p": "p.Leu18Met"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000819837.1",
"gene_symbol": "SRD5A3-AS1",
"hgnc_id": 44138,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-145G>T",
"hgvs_p": null
}
],
"clinvar_disease": "TMEM165-congenital disorder of glycosylation,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "TMEM165-congenital disorder of glycosylation|not specified|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}