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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: 5-154329663-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=154329663&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GALNT10",
"hgnc_id": 19873,
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_198321.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "SAP30L-AS1",
"hgnc_id": 26760,
"hgvs_c": "n.496C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000658072.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 40,
"alphamissense_prediction": null,
"alphamissense_score": 0.0902,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.14,
"chr": "5",
"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": 0.2021041214466095,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 603,
"aa_ref": "V",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5958,
"cdna_start": 627,
"cds_end": null,
"cds_length": 1812,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_198321.4",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000297107.11",
"protein_coding": true,
"protein_id": "NP_938080.1",
"strand": true,
"transcript": "NM_198321.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 603,
"aa_ref": "V",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5958,
"cdna_start": 627,
"cds_end": null,
"cds_length": 1812,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000297107.11",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_198321.4",
"protein_coding": true,
"protein_id": "ENSP00000297107.6",
"strand": true,
"transcript": "ENST00000297107.11",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 632,
"aa_ref": "V",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4311,
"cdna_start": 846,
"cds_end": null,
"cds_length": 1899,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000969502.1",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639561.1",
"strand": true,
"transcript": "ENST00000969502.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 567,
"aa_ref": "V",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5849,
"cdna_start": 626,
"cds_end": null,
"cds_length": 1704,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000917832.1",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587891.1",
"strand": true,
"transcript": "ENST00000917832.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 564,
"aa_ref": "V",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5997,
"cdna_start": 783,
"cds_end": null,
"cds_length": 1695,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000917830.1",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587889.1",
"strand": true,
"transcript": "ENST00000917830.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 541,
"aa_ref": "V",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3778,
"cdna_start": 586,
"cds_end": null,
"cds_length": 1626,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000377661.2",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000366889.2",
"strand": true,
"transcript": "ENST00000377661.2",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 514,
"aa_ref": "V",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5696,
"cdna_start": 632,
"cds_end": null,
"cds_length": 1545,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000917831.1",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587890.1",
"strand": true,
"transcript": "ENST00000917831.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 505,
"aa_ref": "V",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3664,
"cdna_start": 592,
"cds_end": null,
"cds_length": 1518,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000969503.1",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639562.1",
"strand": true,
"transcript": "ENST00000969503.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 366,
"aa_ref": "V",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4344,
"cdna_start": 630,
"cds_end": null,
"cds_length": 1101,
"cds_start": 493,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000425427.6",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "c.493G>A",
"hgvs_p": "p.Val165Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000415210.2",
"strand": true,
"transcript": "ENST00000425427.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 545,
"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": "ENST00000519571.1",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "n.379G>A",
"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": "ENST00000519571.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4359,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000520647.5",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "n.493G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000428573.1",
"strand": true,
"transcript": "ENST00000520647.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 703,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000521781.5",
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"hgvs_c": "n.484G>A",
"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": "ENST00000521781.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4591,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000658072.1",
"gene_hgnc_id": 26760,
"gene_symbol": "SAP30L-AS1",
"hgvs_c": "n.496C>T",
"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": "ENST00000658072.1",
"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": 396,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000519727.5",
"gene_hgnc_id": 26760,
"gene_symbol": "SAP30L-AS1",
"hgvs_c": "n.366+130C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000519727.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs780422451",
"effect": "missense_variant",
"frequency_reference_population": 0.000024804878,
"gene_hgnc_id": 19873,
"gene_symbol": "GALNT10",
"gnomad_exomes_ac": 36,
"gnomad_exomes_af": 0.0000246478,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000263144,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.586,
"pos": 154329663,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.136,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_198321.4"
}
]
}