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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: 16-5025550-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=5025550&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 5025550,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_016256.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1476G>A",
"hgvs_p": "p.Gln492Gln",
"transcript": "NM_016256.4",
"protein_id": "NP_057340.2",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 515,
"cds_start": 1476,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000312251.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016256.4"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1476G>A",
"hgvs_p": "p.Gln492Gln",
"transcript": "ENST00000312251.8",
"protein_id": "ENSP00000310998.3",
"transcript_support_level": 1,
"aa_start": 492,
"aa_end": null,
"aa_length": 515,
"cds_start": 1476,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016256.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000312251.8"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1578G>A",
"hgvs_p": "p.Gln526Gln",
"transcript": "ENST00000948540.1",
"protein_id": "ENSP00000618599.1",
"transcript_support_level": null,
"aa_start": 526,
"aa_end": null,
"aa_length": 549,
"cds_start": 1578,
"cds_end": null,
"cds_length": 1650,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948540.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1416G>A",
"hgvs_p": "p.Gln472Gln",
"transcript": "ENST00000948538.1",
"protein_id": "ENSP00000618597.1",
"transcript_support_level": null,
"aa_start": 472,
"aa_end": null,
"aa_length": 495,
"cds_start": 1416,
"cds_end": null,
"cds_length": 1488,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948538.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1392G>A",
"hgvs_p": "p.Gln464Gln",
"transcript": "ENST00000866188.1",
"protein_id": "ENSP00000536247.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 487,
"cds_start": 1392,
"cds_end": null,
"cds_length": 1464,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866188.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1374G>A",
"hgvs_p": "p.Gln458Gln",
"transcript": "ENST00000381955.7",
"protein_id": "ENSP00000371381.3",
"transcript_support_level": 5,
"aa_start": 458,
"aa_end": null,
"aa_length": 481,
"cds_start": 1374,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381955.7"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1347G>A",
"hgvs_p": "p.Gln449Gln",
"transcript": "ENST00000933627.1",
"protein_id": "ENSP00000603686.1",
"transcript_support_level": null,
"aa_start": 449,
"aa_end": null,
"aa_length": 472,
"cds_start": 1347,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933627.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1344G>A",
"hgvs_p": "p.Gln448Gln",
"transcript": "ENST00000933628.1",
"protein_id": "ENSP00000603687.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 471,
"cds_start": 1344,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933628.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1299G>A",
"hgvs_p": "p.Gln433Gln",
"transcript": "ENST00000948541.1",
"protein_id": "ENSP00000618600.1",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 456,
"cds_start": 1299,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948541.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1245G>A",
"hgvs_p": "p.Gln415Gln",
"transcript": "ENST00000866189.1",
"protein_id": "ENSP00000536248.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 438,
"cds_start": 1245,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866189.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1227G>A",
"hgvs_p": "p.Gln409Gln",
"transcript": "ENST00000866191.1",
"protein_id": "ENSP00000536250.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 432,
"cds_start": 1227,
"cds_end": null,
"cds_length": 1299,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866191.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1098G>A",
"hgvs_p": "p.Gln366Gln",
"transcript": "ENST00000948537.1",
"protein_id": "ENSP00000618596.1",
"transcript_support_level": null,
"aa_start": 366,
"aa_end": null,
"aa_length": 389,
"cds_start": 1098,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948537.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1041G>A",
"hgvs_p": "p.Gln347Gln",
"transcript": "ENST00000866190.1",
"protein_id": "ENSP00000536249.1",
"transcript_support_level": null,
"aa_start": 347,
"aa_end": null,
"aa_length": 370,
"cds_start": 1041,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866190.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Gln338Gln",
"transcript": "ENST00000948539.1",
"protein_id": "ENSP00000618598.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 361,
"cds_start": 1014,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948539.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "c.873G>A",
"hgvs_p": "p.Gln291Gln",
"transcript": "ENST00000563578.5",
"protein_id": "ENSP00000467385.1",
"transcript_support_level": 3,
"aa_start": 291,
"aa_end": null,
"aa_length": 314,
"cds_start": 873,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000563578.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "n.*648G>A",
"hgvs_p": null,
"transcript": "ENST00000562746.5",
"protein_id": "ENSP00000455900.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000562746.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "n.2608G>A",
"hgvs_p": null,
"transcript": "ENST00000564397.5",
"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": "ENST00000564397.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "n.*564G>A",
"hgvs_p": null,
"transcript": "ENST00000649828.1",
"protein_id": "ENSP00000498032.1",
"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": "ENST00000649828.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "n.*648G>A",
"hgvs_p": null,
"transcript": "ENST00000562746.5",
"protein_id": "ENSP00000455900.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000562746.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "n.*564G>A",
"hgvs_p": null,
"transcript": "ENST00000649828.1",
"protein_id": "ENSP00000498032.1",
"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": "ENST00000649828.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"hgvs_c": "n.1204-1G>A",
"hgvs_p": null,
"transcript": "ENST00000568202.5",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000568202.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267072",
"gene_hgnc_id": null,
"hgvs_c": "n.365+14277C>T",
"hgvs_p": null,
"transcript": "ENST00000588778.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000588778.1"
}
],
"gene_symbol": "NAGPA",
"gene_hgnc_id": 17378,
"dbsnp": "rs1413137050",
"frequency_reference_population": 0.0000030989227,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000205312,
"gnomad_genomes_af": 0.0000131344,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5299999713897705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.62,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6,BP7",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_016256.4",
"gene_symbol": "NAGPA",
"hgnc_id": 17378,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1476G>A",
"hgvs_p": "p.Gln492Gln"
},
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000588778.1",
"gene_symbol": "ENSG00000267072",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.365+14277C>T",
"hgvs_p": null
}
],
"clinvar_disease": "NAGPA-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "NAGPA-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}