← Back to variant description
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: 3-125447788-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=125447788&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 125447788,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_003794.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1344C>T",
"hgvs_p": "p.Ser448Ser",
"transcript": "NM_003794.4",
"protein_id": "NP_003785.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 450,
"cds_start": 1344,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000251775.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003794.4"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1344C>T",
"hgvs_p": "p.Ser448Ser",
"transcript": "ENST00000251775.9",
"protein_id": "ENSP00000251775.4",
"transcript_support_level": 1,
"aa_start": 448,
"aa_end": null,
"aa_length": 450,
"cds_start": 1344,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003794.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000251775.9"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1467C>T",
"hgvs_p": "p.Ser489Ser",
"transcript": "ENST00000873377.1",
"protein_id": "ENSP00000543436.1",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 491,
"cds_start": 1467,
"cds_end": null,
"cds_length": 1476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873377.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1461C>T",
"hgvs_p": "p.Ser487Ser",
"transcript": "ENST00000873378.1",
"protein_id": "ENSP00000543437.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 489,
"cds_start": 1461,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873378.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1440C>T",
"hgvs_p": "p.Ser480Ser",
"transcript": "ENST00000873370.1",
"protein_id": "ENSP00000543429.1",
"transcript_support_level": null,
"aa_start": 480,
"aa_end": null,
"aa_length": 482,
"cds_start": 1440,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873370.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1383C>T",
"hgvs_p": "p.Ser461Ser",
"transcript": "ENST00000873374.1",
"protein_id": "ENSP00000543433.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 463,
"cds_start": 1383,
"cds_end": null,
"cds_length": 1392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873374.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1365C>T",
"hgvs_p": "p.Ser455Ser",
"transcript": "ENST00000873372.1",
"protein_id": "ENSP00000543431.1",
"transcript_support_level": null,
"aa_start": 455,
"aa_end": null,
"aa_length": 457,
"cds_start": 1365,
"cds_end": null,
"cds_length": 1374,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873372.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1332C>T",
"hgvs_p": "p.Ser444Ser",
"transcript": "ENST00000945406.1",
"protein_id": "ENSP00000615465.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 446,
"cds_start": 1332,
"cds_end": null,
"cds_length": 1341,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945406.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1317C>T",
"hgvs_p": "p.Ser439Ser",
"transcript": "ENST00000873373.1",
"protein_id": "ENSP00000543432.1",
"transcript_support_level": null,
"aa_start": 439,
"aa_end": null,
"aa_length": 441,
"cds_start": 1317,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873373.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1278C>T",
"hgvs_p": "p.Ser426Ser",
"transcript": "ENST00000873375.1",
"protein_id": "ENSP00000543434.1",
"transcript_support_level": null,
"aa_start": 426,
"aa_end": null,
"aa_length": 428,
"cds_start": 1278,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873375.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1254C>T",
"hgvs_p": "p.Ser418Ser",
"transcript": "ENST00000945404.1",
"protein_id": "ENSP00000615463.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 420,
"cds_start": 1254,
"cds_end": null,
"cds_length": 1263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945404.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1215C>T",
"hgvs_p": "p.Ser405Ser",
"transcript": "ENST00000873371.1",
"protein_id": "ENSP00000543430.1",
"transcript_support_level": null,
"aa_start": 405,
"aa_end": null,
"aa_length": 407,
"cds_start": 1215,
"cds_end": null,
"cds_length": 1224,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873371.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1209C>T",
"hgvs_p": "p.Ser403Ser",
"transcript": "ENST00000873376.1",
"protein_id": "ENSP00000543435.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 405,
"cds_start": 1209,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873376.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.888C>T",
"hgvs_p": "p.Ser296Ser",
"transcript": "ENST00000945405.1",
"protein_id": "ENSP00000615464.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 298,
"cds_start": 888,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945405.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1440C>T",
"hgvs_p": "p.Ser480Ser",
"transcript": "XM_017007414.3",
"protein_id": "XP_016862903.1",
"transcript_support_level": null,
"aa_start": 480,
"aa_end": null,
"aa_length": 482,
"cds_start": 1440,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007414.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "n.*1072C>T",
"hgvs_p": null,
"transcript": "ENST00000471751.5",
"protein_id": "ENSP00000420526.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000471751.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "n.1252C>T",
"hgvs_p": null,
"transcript": "NR_073435.2",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_073435.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "n.*1072C>T",
"hgvs_p": null,
"transcript": "ENST00000471751.5",
"protein_id": "ENSP00000420526.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000471751.5"
}
],
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"dbsnp": "rs1285154096",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.11999999731779099,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.176,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.12,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_003794.4",
"gene_symbol": "SNX4",
"hgnc_id": 11175,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1344C>T",
"hgvs_p": "p.Ser448Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}