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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-120448016-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=120448016&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 120448016,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001122606.1",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "NM_002294.3",
"protein_id": "NP_002285.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 410,
"cds_start": 566,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000200639.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002294.3"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000200639.9",
"protein_id": "ENSP00000200639.4",
"transcript_support_level": 1,
"aa_start": 189,
"aa_end": null,
"aa_length": 410,
"cds_start": 566,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002294.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000200639.9"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000434600.6",
"protein_id": "ENSP00000408411.2",
"transcript_support_level": 1,
"aa_start": 189,
"aa_end": null,
"aa_length": 411,
"cds_start": 566,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000434600.6"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000371335.4",
"protein_id": "ENSP00000360386.4",
"transcript_support_level": 1,
"aa_start": 189,
"aa_end": null,
"aa_length": 410,
"cds_start": 566,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371335.4"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000706600.1",
"protein_id": "ENSP00000516464.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 454,
"cds_start": 566,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000706600.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.692G>A",
"hgvs_p": "p.Cys231Tyr",
"transcript": "ENST00000866856.1",
"protein_id": "ENSP00000536915.1",
"transcript_support_level": null,
"aa_start": 231,
"aa_end": null,
"aa_length": 452,
"cds_start": 692,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866856.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.662G>A",
"hgvs_p": "p.Cys221Tyr",
"transcript": "ENST00000952168.1",
"protein_id": "ENSP00000622227.1",
"transcript_support_level": null,
"aa_start": 221,
"aa_end": null,
"aa_length": 442,
"cds_start": 662,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952168.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.659G>A",
"hgvs_p": "p.Cys220Tyr",
"transcript": "ENST00000866858.1",
"protein_id": "ENSP00000536917.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 441,
"cds_start": 659,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866858.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000952163.1",
"protein_id": "ENSP00000622222.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 436,
"cds_start": 566,
"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": "ENST00000952163.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000866853.1",
"protein_id": "ENSP00000536912.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 426,
"cds_start": 566,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866853.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000866857.1",
"protein_id": "ENSP00000536916.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 415,
"cds_start": 566,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866857.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "NM_001122606.1",
"protein_id": "NP_001116078.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 411,
"cds_start": 566,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001122606.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "NM_013995.2",
"protein_id": "NP_054701.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 410,
"cds_start": 566,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_013995.2"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000952162.1",
"protein_id": "ENSP00000622221.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 409,
"cds_start": 566,
"cds_end": null,
"cds_length": 1230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952162.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.563G>A",
"hgvs_p": "p.Cys188Tyr",
"transcript": "ENST00000952165.1",
"protein_id": "ENSP00000622224.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 409,
"cds_start": 563,
"cds_end": null,
"cds_length": 1230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952165.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000952166.1",
"protein_id": "ENSP00000622225.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 408,
"cds_start": 566,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952166.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.527G>A",
"hgvs_p": "p.Cys176Tyr",
"transcript": "ENST00000866855.1",
"protein_id": "ENSP00000536914.1",
"transcript_support_level": null,
"aa_start": 176,
"aa_end": null,
"aa_length": 397,
"cds_start": 527,
"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": "ENST00000866855.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.428G>A",
"hgvs_p": "p.Cys143Tyr",
"transcript": "ENST00000952167.1",
"protein_id": "ENSP00000622226.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 364,
"cds_start": 428,
"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": "ENST00000952167.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "ENST00000952164.1",
"protein_id": "ENSP00000622223.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 355,
"cds_start": 566,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952164.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Cys78Tyr",
"transcript": "ENST00000866854.1",
"protein_id": "ENSP00000536913.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 299,
"cds_start": 233,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866854.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "c.65-6122G>A",
"hgvs_p": null,
"transcript": "ENST00000936274.1",
"protein_id": "ENSP00000606333.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 122,
"cds_start": null,
"cds_end": null,
"cds_length": 369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936274.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"hgvs_c": "n.107G>A",
"hgvs_p": null,
"transcript": "ENST00000486593.5",
"protein_id": "ENSP00000431526.1",
"transcript_support_level": 5,
"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": "ENST00000486593.5"
}
],
"gene_symbol": "LAMP2",
"gene_hgnc_id": 6501,
"dbsnp": "rs750457485",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 9.12598e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11095406115055084,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "CardioboostCm",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.404,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9532,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.387,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001122606.1",
"gene_symbol": "LAMP2",
"hgnc_id": 6501,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr"
}
],
"clinvar_disease": "Danon disease",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Danon disease",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}