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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: 7-128852998-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=128852998&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "FLNC",
"hgnc_id": 3756,
"hgvs_c": "c.6175G>A",
"hgvs_p": "p.Val2059Met",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_001458.5",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "FLNC-AS1",
"hgnc_id": 53474,
"hgvs_c": "n.215+287C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000469965.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 1968,
"alphamissense_prediction": null,
"alphamissense_score": 0.0952,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.28,
"chr": "7",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": " Dominant,Cardiomyopathy,Cardiovascular phenotype,Dilated Cardiomyopathy,Distal myopathy with posterior leg and anterior hand involvement,FLNC-related disorder,Hypertrophic cardiomyopathy 26,Myofibrillar myopathy 5,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:8 B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.021668076515197754,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 2725,
"aa_ref": "V",
"aa_start": 2059,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9159,
"cdna_start": 6407,
"cds_end": null,
"cds_length": 8178,
"cds_start": 6175,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "NM_001458.5",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "c.6175G>A",
"hgvs_p": "p.Val2059Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000325888.13",
"protein_coding": true,
"protein_id": "NP_001449.3",
"strand": true,
"transcript": "NM_001458.5",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 2725,
"aa_ref": "V",
"aa_start": 2059,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9159,
"cdna_start": 6407,
"cds_end": null,
"cds_length": 8178,
"cds_start": 6175,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "ENST00000325888.13",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "c.6175G>A",
"hgvs_p": "p.Val2059Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001458.5",
"protein_coding": true,
"protein_id": "ENSP00000327145.8",
"strand": true,
"transcript": "ENST00000325888.13",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 2692,
"aa_ref": "V",
"aa_start": 2026,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9042,
"cdna_start": 6288,
"cds_end": null,
"cds_length": 8079,
"cds_start": 6076,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "ENST00000346177.6",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "c.6076G>A",
"hgvs_p": "p.Val2026Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000344002.6",
"strand": true,
"transcript": "ENST00000346177.6",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 2692,
"aa_ref": "V",
"aa_start": 2026,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9060,
"cdna_start": 6308,
"cds_end": null,
"cds_length": 8079,
"cds_start": 6076,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "NM_001127487.2",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "c.6076G>A",
"hgvs_p": "p.Val2026Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001120959.1",
"strand": true,
"transcript": "NM_001127487.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 2691,
"aa_ref": "V",
"aa_start": 2025,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9055,
"cdna_start": 6303,
"cds_end": null,
"cds_length": 8076,
"cds_start": 6073,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "ENST00000950263.1",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "c.6073G>A",
"hgvs_p": "p.Val2025Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620322.1",
"strand": true,
"transcript": "ENST00000950263.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 2679,
"aa_ref": "V",
"aa_start": 2059,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9023,
"cdna_start": 6407,
"cds_end": null,
"cds_length": 8040,
"cds_start": 6175,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "ENST00000714183.1",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "c.6175G>A",
"hgvs_p": "p.Val2059Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519472.1",
"strand": true,
"transcript": "ENST00000714183.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 2599,
"aa_ref": "V",
"aa_start": 1933,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8878,
"cdna_start": 6123,
"cds_end": null,
"cds_length": 7800,
"cds_start": 5797,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "ENST00000950262.1",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "c.5797G>A",
"hgvs_p": "p.Val1933Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620321.1",
"strand": true,
"transcript": "ENST00000950262.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 2584,
"aa_ref": "V",
"aa_start": 1963,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8874,
"cdna_start": 6116,
"cds_end": null,
"cds_length": 7755,
"cds_start": 5887,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000714184.1",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "c.5887G>A",
"hgvs_p": "p.Val1963Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519473.1",
"strand": true,
"transcript": "ENST00000714184.1",
"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": 559,
"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": "ENST00000469965.1",
"gene_hgnc_id": 53474,
"gene_symbol": "FLNC-AS1",
"hgvs_c": "n.215+287C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000469965.1",
"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": 9476,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 47,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000714185.1",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "n.*1246+46G>A",
"hgvs_p": null,
"intron_rank": 36,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519474.1",
"strand": true,
"transcript": "ENST00000714185.1",
"transcript_support_level": null
},
{
"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": 9079,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 48,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000714186.1",
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"hgvs_c": "n.6129+46G>A",
"hgvs_p": null,
"intron_rank": 37,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519475.1",
"strand": true,
"transcript": "ENST00000714186.1",
"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": 559,
"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": "NR_149055.1",
"gene_hgnc_id": 53474,
"gene_symbol": "FLNC-AS1",
"hgvs_c": "n.215+287C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_149055.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201333104",
"effect": "missense_variant",
"frequency_reference_population": 0.0012197994,
"gene_hgnc_id": 3756,
"gene_symbol": "FLNC",
"gnomad_exomes_ac": 1858,
"gnomad_exomes_af": 0.00127164,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 110,
"gnomad_genomes_af": 0.000722354,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "Hypertrophic cardiomyopathy 26|Distal myopathy with posterior leg and anterior hand involvement|not provided|Myofibrillar myopathy 5|Distal myopathy with posterior leg and anterior hand involvement;Myofibrillar myopathy 5;Hypertrophic cardiomyopathy 26;Dilated Cardiomyopathy, Dominant|Cardiovascular phenotype|not specified|Cardiomyopathy|FLNC-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.561,
"pos": 128852998,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.326,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001458.5"
}
]
}