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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: 19-55174612-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=55174612&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 55174612,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003180.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.865A>G",
"hgvs_p": "p.Lys289Glu",
"transcript": "NM_003180.3",
"protein_id": "NP_003171.2",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 386,
"cds_start": 865,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000354308.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003180.3"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.865A>G",
"hgvs_p": "p.Lys289Glu",
"transcript": "ENST00000354308.8",
"protein_id": "ENSP00000346265.2",
"transcript_support_level": 1,
"aa_start": 289,
"aa_end": null,
"aa_length": 386,
"cds_start": 865,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003180.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000354308.8"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.865A>G",
"hgvs_p": "p.Lys289Glu",
"transcript": "ENST00000537500.5",
"protein_id": "ENSP00000442896.1",
"transcript_support_level": 2,
"aa_start": 289,
"aa_end": null,
"aa_length": 386,
"cds_start": 865,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000537500.5"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.865A>G",
"hgvs_p": "p.Lys289Glu",
"transcript": "ENST00000868688.1",
"protein_id": "ENSP00000538747.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 386,
"cds_start": 865,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868688.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.865A>G",
"hgvs_p": "p.Lys289Glu",
"transcript": "ENST00000948087.1",
"protein_id": "ENSP00000618146.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 386,
"cds_start": 865,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948087.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.862A>G",
"hgvs_p": "p.Lys288Glu",
"transcript": "ENST00000868679.1",
"protein_id": "ENSP00000538739.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 385,
"cds_start": 862,
"cds_end": null,
"cds_length": 1158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868679.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.862A>G",
"hgvs_p": "p.Lys288Glu",
"transcript": "ENST00000868681.1",
"protein_id": "ENSP00000538740.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 385,
"cds_start": 862,
"cds_end": null,
"cds_length": 1158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868681.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.862A>G",
"hgvs_p": "p.Lys288Glu",
"transcript": "ENST00000868689.1",
"protein_id": "ENSP00000538748.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 385,
"cds_start": 862,
"cds_end": null,
"cds_length": 1158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868689.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.859A>G",
"hgvs_p": "p.Lys287Glu",
"transcript": "ENST00000868686.1",
"protein_id": "ENSP00000538746.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 384,
"cds_start": 859,
"cds_end": null,
"cds_length": 1155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868686.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.856A>G",
"hgvs_p": "p.Lys286Glu",
"transcript": "ENST00000868684.1",
"protein_id": "ENSP00000538743.1",
"transcript_support_level": null,
"aa_start": 286,
"aa_end": null,
"aa_length": 383,
"cds_start": 856,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868684.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.853A>G",
"hgvs_p": "p.Lys285Glu",
"transcript": "NM_001297774.2",
"protein_id": "NP_001284703.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 382,
"cds_start": 853,
"cds_end": null,
"cds_length": 1149,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001297774.2"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.853A>G",
"hgvs_p": "p.Lys285Glu",
"transcript": "ENST00000590851.5",
"protein_id": "ENSP00000465576.1",
"transcript_support_level": 2,
"aa_start": 285,
"aa_end": null,
"aa_length": 382,
"cds_start": 853,
"cds_end": null,
"cds_length": 1149,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590851.5"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.61A>G",
"hgvs_p": "p.Lys21Glu",
"transcript": "ENST00000587067.1",
"protein_id": "ENSP00000465304.1",
"transcript_support_level": 2,
"aa_start": 21,
"aa_end": null,
"aa_length": 66,
"cds_start": 61,
"cds_end": null,
"cds_length": 201,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587067.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.865A>G",
"hgvs_p": "p.Lys289Glu",
"transcript": "XM_006723339.4",
"protein_id": "XP_006723402.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 386,
"cds_start": 865,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006723339.4"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.865A>G",
"hgvs_p": "p.Lys289Glu",
"transcript": "XM_017027175.2",
"protein_id": "XP_016882664.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 386,
"cds_start": 865,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027175.2"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.865A>G",
"hgvs_p": "p.Lys289Glu",
"transcript": "XM_047439256.1",
"protein_id": "XP_047295212.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 386,
"cds_start": 865,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439256.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.862A>G",
"hgvs_p": "p.Lys288Glu",
"transcript": "XM_047439257.1",
"protein_id": "XP_047295213.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 385,
"cds_start": 862,
"cds_end": null,
"cds_length": 1158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439257.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.856A>G",
"hgvs_p": "p.Lys286Glu",
"transcript": "XM_006723341.4",
"protein_id": "XP_006723404.1",
"transcript_support_level": null,
"aa_start": 286,
"aa_end": null,
"aa_length": 383,
"cds_start": 856,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006723341.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "n.746A>G",
"hgvs_p": null,
"transcript": "ENST00000588305.5",
"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": "ENST00000588305.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "n.330A>G",
"hgvs_p": null,
"transcript": "ENST00000592956.1",
"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": "ENST00000592956.1"
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "DNAAF3-AS1",
"gene_hgnc_id": 55292,
"hgvs_c": "n.1187-2472T>C",
"hgvs_p": null,
"transcript": "ENST00000591665.1",
"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": "pseudogene",
"feature": "ENST00000591665.1"
},
{
"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": "DNAAF3-AS1",
"gene_hgnc_id": 55292,
"hgvs_c": "n.355-2472T>C",
"hgvs_p": null,
"transcript": "ENST00000805275.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000805275.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"hgvs_c": "c.-48A>G",
"hgvs_p": null,
"transcript": "ENST00000590859.1",
"protein_id": "ENSP00000469874.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 21,
"cds_start": null,
"cds_end": null,
"cds_length": 66,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590859.1"
}
],
"gene_symbol": "SYT5",
"gene_hgnc_id": 11513,
"dbsnp": "rs750454898",
"frequency_reference_population": 0.000030361161,
"hom_count_reference_population": 0,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000300988,
"gnomad_genomes_af": 0.0000328839,
"gnomad_exomes_ac": 44,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3209652900695801,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.281,
"revel_prediction": "Benign",
"alphamissense_score": 0.9376,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.185,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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_003180.3",
"gene_symbol": "SYT5",
"hgnc_id": 11513,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.865A>G",
"hgvs_p": "p.Lys289Glu"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000591665.1",
"gene_symbol": "DNAAF3-AS1",
"hgnc_id": 55292,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1187-2472T>C",
"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
}