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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: 16-69322560-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=69322560&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 69322560,
"ref": "G",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_013245.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.1072G>C",
"hgvs_p": "p.Val358Leu",
"transcript": "NM_013245.3",
"protein_id": "NP_037377.1",
"transcript_support_level": null,
"aa_start": 358,
"aa_end": null,
"aa_length": 437,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000254950.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_013245.3"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.1072G>C",
"hgvs_p": "p.Val358Leu",
"transcript": "ENST00000254950.13",
"protein_id": "ENSP00000254950.11",
"transcript_support_level": 1,
"aa_start": 358,
"aa_end": null,
"aa_length": 437,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_013245.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000254950.13"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000260914",
"gene_hgnc_id": null,
"hgvs_c": "c.1144G>C",
"hgvs_p": "p.Val382Leu",
"transcript": "ENST00000570054.3",
"protein_id": "ENSP00000461295.3",
"transcript_support_level": 5,
"aa_start": 382,
"aa_end": null,
"aa_length": 427,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000570054.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.1350G>C",
"hgvs_p": null,
"transcript": "ENST00000566354.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000566354.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.1069G>C",
"hgvs_p": "p.Val357Leu",
"transcript": "ENST00000714474.1",
"protein_id": "ENSP00000519731.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 436,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1311,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714474.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.1024G>C",
"hgvs_p": "p.Val342Leu",
"transcript": "ENST00000907004.1",
"protein_id": "ENSP00000577063.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 421,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907004.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.952G>C",
"hgvs_p": "p.Val318Leu",
"transcript": "ENST00000949393.1",
"protein_id": "ENSP00000619452.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 397,
"cds_start": 952,
"cds_end": null,
"cds_length": 1194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949393.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.949G>C",
"hgvs_p": "p.Val317Leu",
"transcript": "ENST00000714473.1",
"protein_id": "ENSP00000519730.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 396,
"cds_start": 949,
"cds_end": null,
"cds_length": 1191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714473.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.733G>C",
"hgvs_p": "p.Val245Leu",
"transcript": "ENST00000714477.1",
"protein_id": "ENSP00000519734.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 324,
"cds_start": 733,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714477.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.733G>C",
"hgvs_p": "p.Val245Leu",
"transcript": "ENST00000714480.1",
"protein_id": "ENSP00000519737.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 324,
"cds_start": 733,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714480.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.733G>C",
"hgvs_p": "p.Val245Leu",
"transcript": "ENST00000714482.1",
"protein_id": "ENSP00000519739.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 324,
"cds_start": 733,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714482.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.733G>C",
"hgvs_p": "p.Val245Leu",
"transcript": "ENST00000714483.1",
"protein_id": "ENSP00000519740.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 324,
"cds_start": 733,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714483.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "c.*1023C>G",
"hgvs_p": null,
"transcript": "ENST00000562595.5",
"protein_id": "ENSP00000456705.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 222,
"cds_start": null,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000562595.5"
},
{
"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": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.1034-67G>C",
"hgvs_p": null,
"transcript": "ENST00000949392.1",
"protein_id": "ENSP00000619451.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 402,
"cds_start": null,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949392.1"
},
{
"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": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.1071+1290G>C",
"hgvs_p": null,
"transcript": "ENST00000949394.1",
"protein_id": "ENSP00000619453.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 390,
"cds_start": null,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949394.1"
},
{
"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": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.1072-67G>C",
"hgvs_p": null,
"transcript": "ENST00000714476.1",
"protein_id": "ENSP00000519733.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 364,
"cds_start": null,
"cds_end": null,
"cds_length": 1095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714476.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*791G>C",
"hgvs_p": null,
"transcript": "ENST00000714472.1",
"protein_id": "ENSP00000519729.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000714472.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.1034G>C",
"hgvs_p": null,
"transcript": "ENST00000714475.1",
"protein_id": "ENSP00000519732.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000714475.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*1032G>C",
"hgvs_p": null,
"transcript": "ENST00000714478.1",
"protein_id": "ENSP00000519735.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000714478.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.1088G>C",
"hgvs_p": null,
"transcript": "ENST00000714479.1",
"protein_id": "ENSP00000519736.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000714479.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*480G>C",
"hgvs_p": null,
"transcript": "ENST00000714481.1",
"protein_id": "ENSP00000519738.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000714481.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*1215G>C",
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{
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],
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"gnomad_exomes_homalt": 0,
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"computational_prediction_selected": "Uncertain_significance",
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"splice_score_selected": 0.9200000166893005,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
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"revel_prediction": "Uncertain_significance",
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"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
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"phylop100way_prediction": "Uncertain_significance",
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"spliceai_max_prediction": "Uncertain_significance",
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"dbscsnv_ada_prediction": "Pathogenic",
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"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
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"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_013245.3",
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"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR",
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{
"score": 3,
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"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000570054.3",
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"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1144G>C",
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},
{
"score": 3,
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"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000562595.5",
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"inheritance_mode": "AR",
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}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}