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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: 6-47577102-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=47577102&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 47577102,
"ref": "A",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_012120.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.902A>T",
"hgvs_p": "p.Lys301Met",
"transcript": "NM_012120.3",
"protein_id": "NP_036252.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 639,
"cds_start": 902,
"cds_end": null,
"cds_length": 1920,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000359314.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012120.3"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.902A>T",
"hgvs_p": "p.Lys301Met",
"transcript": "ENST00000359314.5",
"protein_id": "ENSP00000352264.5",
"transcript_support_level": 1,
"aa_start": 301,
"aa_end": null,
"aa_length": 639,
"cds_start": 902,
"cds_end": null,
"cds_length": 1920,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012120.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000359314.5"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.905A>T",
"hgvs_p": "p.Lys302Met",
"transcript": "ENST00000865253.1",
"protein_id": "ENSP00000535312.1",
"transcript_support_level": null,
"aa_start": 302,
"aa_end": null,
"aa_length": 640,
"cds_start": 905,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865253.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.902A>T",
"hgvs_p": "p.Lys301Met",
"transcript": "ENST00000931707.1",
"protein_id": "ENSP00000601766.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 636,
"cds_start": 902,
"cds_end": null,
"cds_length": 1911,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931707.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.893A>T",
"hgvs_p": "p.Lys298Met",
"transcript": "ENST00000931708.1",
"protein_id": "ENSP00000601767.1",
"transcript_support_level": null,
"aa_start": 298,
"aa_end": null,
"aa_length": 636,
"cds_start": 893,
"cds_end": null,
"cds_length": 1911,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931708.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.890A>T",
"hgvs_p": "p.Lys297Met",
"transcript": "ENST00000865252.1",
"protein_id": "ENSP00000535311.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 635,
"cds_start": 890,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865252.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.902A>T",
"hgvs_p": "p.Lys301Met",
"transcript": "ENST00000931709.1",
"protein_id": "ENSP00000601768.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 631,
"cds_start": 902,
"cds_end": null,
"cds_length": 1896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931709.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.902A>T",
"hgvs_p": "p.Lys301Met",
"transcript": "ENST00000960842.1",
"protein_id": "ENSP00000630901.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 618,
"cds_start": 902,
"cds_end": null,
"cds_length": 1857,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960842.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.365A>T",
"hgvs_p": "p.Lys122Met",
"transcript": "ENST00000865254.1",
"protein_id": "ENSP00000535313.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 460,
"cds_start": 365,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865254.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.890A>T",
"hgvs_p": "p.Lys297Met",
"transcript": "XM_005248976.2",
"protein_id": "XP_005249033.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 635,
"cds_start": 890,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005248976.2"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.755A>T",
"hgvs_p": "p.Lys252Met",
"transcript": "XM_011514449.3",
"protein_id": "XP_011512751.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 590,
"cds_start": 755,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514449.3"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.902A>T",
"hgvs_p": "p.Lys301Met",
"transcript": "XM_017010641.2",
"protein_id": "XP_016866130.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 476,
"cds_start": 902,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017010641.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "c.420+32396A>T",
"hgvs_p": null,
"transcript": "ENST00000960843.1",
"protein_id": "ENSP00000630902.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": null,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960843.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"hgvs_c": "n.184A>T",
"hgvs_p": null,
"transcript": "ENST00000463175.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000463175.1"
}
],
"gene_symbol": "CD2AP",
"gene_hgnc_id": 14258,
"dbsnp": "rs141778404",
"frequency_reference_population": 0.0001904008,
"hom_count_reference_population": 5,
"allele_count_reference_population": 279,
"gnomad_exomes_af": 0.000195725,
"gnomad_genomes_af": 0.000144488,
"gnomad_exomes_ac": 257,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7232401967048645,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.6499999761581421,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.798,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5494,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.139,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.987907400604497,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BS1,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_012120.3",
"gene_symbol": "CD2AP",
"hgnc_id": 14258,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.902A>T",
"hgvs_p": "p.Lys301Met"
}
],
"clinvar_disease": " susceptibility to,Focal segmental glomerulosclerosis 3,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "not specified|Focal segmental glomerulosclerosis 3, susceptibility to|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}