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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: 8-43197848-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=43197848&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 43197848,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000379644.9",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.1622C>T",
"hgvs_p": "p.Ser541Leu",
"transcript": "NM_152419.3",
"protein_id": "NP_689632.2",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 635,
"cds_start": 1622,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 1655,
"cdna_end": null,
"cdna_length": 5227,
"mane_select": "ENST00000379644.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.1622C>T",
"hgvs_p": "p.Ser541Leu",
"transcript": "ENST00000379644.9",
"protein_id": "ENSP00000368965.4",
"transcript_support_level": 2,
"aa_start": 541,
"aa_end": null,
"aa_length": 635,
"cds_start": 1622,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 1655,
"cdna_end": null,
"cdna_length": 5227,
"mane_select": "NM_152419.3",
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "n.938C>T",
"hgvs_p": null,
"transcript": "ENST00000519705.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 1513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.1709C>T",
"hgvs_p": "p.Ser570Leu",
"transcript": "NM_001363227.2",
"protein_id": "NP_001350156.1",
"transcript_support_level": null,
"aa_start": 570,
"aa_end": null,
"aa_length": 664,
"cds_start": 1709,
"cds_end": null,
"cds_length": 1995,
"cdna_start": 1742,
"cdna_end": null,
"cdna_length": 5314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.1430C>T",
"hgvs_p": "p.Ser477Leu",
"transcript": "NM_001363228.2",
"protein_id": "NP_001350157.1",
"transcript_support_level": null,
"aa_start": 477,
"aa_end": null,
"aa_length": 571,
"cds_start": 1430,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 1463,
"cdna_end": null,
"cdna_length": 5035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.773C>T",
"hgvs_p": "p.Ser258Leu",
"transcript": "ENST00000521576.1",
"protein_id": "ENSP00000429029.1",
"transcript_support_level": 2,
"aa_start": 258,
"aa_end": null,
"aa_length": 352,
"cds_start": 773,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 1060,
"cdna_end": null,
"cdna_length": 2332,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.758C>T",
"hgvs_p": "p.Ser253Leu",
"transcript": "NM_001363229.2",
"protein_id": "NP_001350158.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 347,
"cds_start": 758,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 1624,
"cdna_end": null,
"cdna_length": 5196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.1733C>T",
"hgvs_p": "p.Ser578Leu",
"transcript": "XM_005273409.2",
"protein_id": "XP_005273466.1",
"transcript_support_level": null,
"aa_start": 578,
"aa_end": null,
"aa_length": 672,
"cds_start": 1733,
"cds_end": null,
"cds_length": 2019,
"cdna_start": 1766,
"cdna_end": null,
"cdna_length": 5338,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.1541C>T",
"hgvs_p": "p.Ser514Leu",
"transcript": "XM_005273411.2",
"protein_id": "XP_005273468.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 608,
"cds_start": 1541,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1574,
"cdna_end": null,
"cdna_length": 5146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.869C>T",
"hgvs_p": "p.Ser290Leu",
"transcript": "XM_047421388.1",
"protein_id": "XP_047277344.1",
"transcript_support_level": null,
"aa_start": 290,
"aa_end": null,
"aa_length": 384,
"cds_start": 869,
"cds_end": null,
"cds_length": 1155,
"cdna_start": 953,
"cdna_end": null,
"cdna_length": 4525,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "n.1935C>T",
"hgvs_p": null,
"transcript": "ENST00000523989.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 1994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"dbsnp": "rs756310864",
"frequency_reference_population": 0.00004337916,
"hom_count_reference_population": 0,
"allele_count_reference_population": 70,
"gnomad_exomes_af": 0.0000437913,
"gnomad_genomes_af": 0.0000394218,
"gnomad_exomes_ac": 64,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.964691698551178,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.859,
"revel_prediction": "Pathogenic",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.447,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000379644.9",
"gene_symbol": "HGSNAT",
"hgnc_id": 26527,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1622C>T",
"hgvs_p": "p.Ser541Leu"
}
],
"clinvar_disease": " MPS-III-C,Mucopolysaccharidosis,Retinal dystrophy,Retinitis pigmentosa 73,Sanfilippo syndrome,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:3",
"phenotype_combined": "Retinitis pigmentosa 73;Mucopolysaccharidosis, MPS-III-C|Retinal dystrophy|Mucopolysaccharidosis, MPS-III-C|Sanfilippo syndrome|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}