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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: 3-169983170-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=169983170&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 169983170,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003262.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.466C>T",
"hgvs_p": "p.Pro156Ser",
"transcript": "NM_003262.4",
"protein_id": "NP_003253.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 399,
"cds_start": 466,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000337002.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003262.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.466C>T",
"hgvs_p": "p.Pro156Ser",
"transcript": "ENST00000337002.9",
"protein_id": "ENSP00000337688.4",
"transcript_support_level": 1,
"aa_start": 156,
"aa_end": null,
"aa_length": 399,
"cds_start": 466,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003262.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000337002.9"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.466C>T",
"hgvs_p": "p.Pro156Ser",
"transcript": "ENST00000480708.5",
"protein_id": "ENSP00000420331.1",
"transcript_support_level": 1,
"aa_start": 156,
"aa_end": null,
"aa_length": 399,
"cds_start": 466,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000480708.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.574C>T",
"hgvs_p": "p.Pro192Ser",
"transcript": "ENST00000870859.1",
"protein_id": "ENSP00000540918.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 435,
"cds_start": 574,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870859.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.559C>T",
"hgvs_p": "p.Pro187Ser",
"transcript": "ENST00000870865.1",
"protein_id": "ENSP00000540924.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 430,
"cds_start": 559,
"cds_end": null,
"cds_length": 1293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870865.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Pro157Ser",
"transcript": "ENST00000870860.1",
"protein_id": "ENSP00000540919.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 400,
"cds_start": 469,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870860.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.463C>T",
"hgvs_p": "p.Pro155Ser",
"transcript": "ENST00000932400.1",
"protein_id": "ENSP00000602459.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 398,
"cds_start": 463,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932400.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.442C>T",
"hgvs_p": "p.Pro148Ser",
"transcript": "ENST00000870862.1",
"protein_id": "ENSP00000540921.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 391,
"cds_start": 442,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870862.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.466C>T",
"hgvs_p": "p.Pro156Ser",
"transcript": "ENST00000870863.1",
"protein_id": "ENSP00000540922.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 359,
"cds_start": 466,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870863.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Pro16Ser",
"transcript": "ENST00000870864.1",
"protein_id": "ENSP00000540923.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 259,
"cds_start": 46,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870864.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.352C>T",
"hgvs_p": "p.Pro118Ser",
"transcript": "XM_011513114.4",
"protein_id": "XP_011511416.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 361,
"cds_start": 352,
"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": "XM_011513114.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.352C>T",
"hgvs_p": "p.Pro118Ser",
"transcript": "XM_047448819.1",
"protein_id": "XP_047304775.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 361,
"cds_start": 352,
"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": "XM_047448819.1"
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.456+259C>T",
"hgvs_p": null,
"transcript": "ENST00000932401.1",
"protein_id": "ENSP00000602460.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": null,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932401.1"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.146-5070C>T",
"hgvs_p": null,
"transcript": "ENST00000932402.1",
"protein_id": "ENSP00000602461.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 244,
"cds_start": null,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932402.1"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.37-2635C>T",
"hgvs_p": null,
"transcript": "ENST00000870858.1",
"protein_id": "ENSP00000540917.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 228,
"cds_start": null,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870858.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "c.145+7454C>T",
"hgvs_p": null,
"transcript": "ENST00000870861.1",
"protein_id": "ENSP00000540920.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 204,
"cds_start": null,
"cds_end": null,
"cds_length": 615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870861.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "n.*278C>T",
"hgvs_p": null,
"transcript": "ENST00000460513.5",
"protein_id": "ENSP00000419319.1",
"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": "ENST00000460513.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "n.*207C>T",
"hgvs_p": null,
"transcript": "ENST00000469515.6",
"protein_id": "ENSP00000418342.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000469515.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "n.53C>T",
"hgvs_p": null,
"transcript": "ENST00000469890.1",
"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": "ENST00000469890.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "n.463C>T",
"hgvs_p": null,
"transcript": "ENST00000481435.5",
"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": "ENST00000481435.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "n.*278C>T",
"hgvs_p": null,
"transcript": "ENST00000460513.5",
"protein_id": "ENSP00000419319.1",
"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": "ENST00000460513.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"hgvs_c": "n.*207C>T",
"hgvs_p": null,
"transcript": "ENST00000469515.6",
"protein_id": "ENSP00000418342.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000469515.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SEC62-AS1",
"gene_hgnc_id": 40586,
"hgvs_c": "n.320+2226G>A",
"hgvs_p": null,
"transcript": "ENST00000479626.1",
"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": "pseudogene",
"feature": "ENST00000479626.1"
}
],
"gene_symbol": "SEC62",
"gene_hgnc_id": 11846,
"dbsnp": "rs1349632594",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.33443892002105713,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.226,
"revel_prediction": "Benign",
"alphamissense_score": 0.2522,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.187,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003262.4",
"gene_symbol": "SEC62",
"hgnc_id": 11846,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.466C>T",
"hgvs_p": "p.Pro156Ser"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000479626.1",
"gene_symbol": "SEC62-AS1",
"hgnc_id": 40586,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.320+2226G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}