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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: X-154366562-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=154366562&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 154366562,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "ENST00000369850.10",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "c.1065G>A",
"hgvs_p": "p.Lys355Lys",
"transcript": "NM_001110556.2",
"protein_id": "NP_001104026.1",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 2647,
"cds_start": 1065,
"cds_end": null,
"cds_length": 7944,
"cdna_start": 1310,
"cdna_end": null,
"cdna_length": 8507,
"mane_select": "ENST00000369850.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "c.1065G>A",
"hgvs_p": "p.Lys355Lys",
"transcript": "ENST00000369850.10",
"protein_id": "ENSP00000358866.3",
"transcript_support_level": 1,
"aa_start": 355,
"aa_end": null,
"aa_length": 2647,
"cds_start": 1065,
"cds_end": null,
"cds_length": 7944,
"cdna_start": 1310,
"cdna_end": null,
"cdna_length": 8507,
"mane_select": "NM_001110556.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "c.1065G>A",
"hgvs_p": "p.Lys355Lys",
"transcript": "ENST00000360319.9",
"protein_id": "ENSP00000353467.4",
"transcript_support_level": 1,
"aa_start": 355,
"aa_end": null,
"aa_length": 2639,
"cds_start": 1065,
"cds_end": null,
"cds_length": 7920,
"cdna_start": 1103,
"cdna_end": null,
"cdna_length": 8278,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "c.984G>A",
"hgvs_p": "p.Lys328Lys",
"transcript": "ENST00000369856.8",
"protein_id": "ENSP00000358872.4",
"transcript_support_level": 1,
"aa_start": 328,
"aa_end": null,
"aa_length": 2620,
"cds_start": 984,
"cds_end": null,
"cds_length": 7863,
"cdna_start": 1042,
"cdna_end": null,
"cdna_length": 8240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "c.1065G>A",
"hgvs_p": "p.Lys355Lys",
"transcript": "NM_001456.4",
"protein_id": "NP_001447.2",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 2639,
"cds_start": 1065,
"cds_end": null,
"cds_length": 7920,
"cdna_start": 1310,
"cdna_end": null,
"cdna_length": 8483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "c.1065G>A",
"hgvs_p": "p.Lys355Lys",
"transcript": "ENST00000422373.6",
"protein_id": "ENSP00000416926.2",
"transcript_support_level": 5,
"aa_start": 355,
"aa_end": null,
"aa_length": 1574,
"cds_start": 1065,
"cds_end": null,
"cds_length": 4725,
"cdna_start": 1103,
"cdna_end": null,
"cdna_length": 5083,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "n.1023G>A",
"hgvs_p": null,
"transcript": "ENST00000420627.5",
"protein_id": "ENSP00000408921.1",
"transcript_support_level": 5,
"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": 8225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "n.1065G>A",
"hgvs_p": null,
"transcript": "ENST00000610817.5",
"protein_id": "ENSP00000480593.2",
"transcript_support_level": 5,
"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": 8319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "n.1065G>A",
"hgvs_p": null,
"transcript": "ENST00000676696.1",
"protein_id": "ENSP00000503392.1",
"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": 8541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"hgvs_c": "c.-230G>A",
"hgvs_p": null,
"transcript": "ENST00000673639.2",
"protein_id": "ENSP00000501210.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 95,
"cds_start": -4,
"cds_end": null,
"cds_length": 288,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 435,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FLNA",
"gene_hgnc_id": 3754,
"dbsnp": "rs1557179325",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.2199999988079071,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9800000190734863,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.903,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.34,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.998664200625118,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000369850.10",
"gene_symbol": "FLNA",
"hgnc_id": 3754,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "XL,AD,AR",
"hgvs_c": "c.1065G>A",
"hgvs_p": "p.Lys355Lys"
}
],
"clinvar_disease": " X-linked dominant, periventricular, type II,Frontometaphyseal dysplasia,Heterotopia,Melnick-Needles syndrome,Oto-palato-digital syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Heterotopia, periventricular, X-linked dominant|Melnick-Needles syndrome;Frontometaphyseal dysplasia;Oto-palato-digital syndrome, type II;Heterotopia, periventricular, X-linked dominant",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}