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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: 6-42935645-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=42935645&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 42935645,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001318842.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.347G>C",
"hgvs_p": "p.Arg116Thr",
"transcript": "NM_006586.5",
"protein_id": "NP_006577.2",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 278,
"cds_start": 347,
"cds_end": null,
"cds_length": 837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000372836.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006586.5"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.347G>C",
"hgvs_p": "p.Arg116Thr",
"transcript": "ENST00000372836.5",
"protein_id": "ENSP00000361926.4",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 278,
"cds_start": 347,
"cds_end": null,
"cds_length": 837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006586.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372836.5"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.509G>C",
"hgvs_p": "p.Arg170Thr",
"transcript": "ENST00000893179.1",
"protein_id": "ENSP00000563238.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 332,
"cds_start": 509,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893179.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.509G>C",
"hgvs_p": "p.Arg170Thr",
"transcript": "ENST00000924680.1",
"protein_id": "ENSP00000594739.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 332,
"cds_start": 509,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924680.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.446G>C",
"hgvs_p": "p.Arg149Thr",
"transcript": "NM_001318842.1",
"protein_id": "NP_001305771.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 311,
"cds_start": 446,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318842.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.446G>C",
"hgvs_p": "p.Arg149Thr",
"transcript": "ENST00000924677.1",
"protein_id": "ENSP00000594736.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 311,
"cds_start": 446,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924677.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.422G>C",
"hgvs_p": "p.Arg141Thr",
"transcript": "ENST00000924679.1",
"protein_id": "ENSP00000594738.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 303,
"cds_start": 422,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924679.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.389G>C",
"hgvs_p": "p.Arg130Thr",
"transcript": "ENST00000893180.1",
"protein_id": "ENSP00000563239.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 292,
"cds_start": 389,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893180.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.509G>C",
"hgvs_p": "p.Arg170Thr",
"transcript": "ENST00000945354.1",
"protein_id": "ENSP00000615413.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 291,
"cds_start": 509,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945354.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.344G>C",
"hgvs_p": "p.Arg115Thr",
"transcript": "ENST00000945352.1",
"protein_id": "ENSP00000615411.1",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 277,
"cds_start": 344,
"cds_end": null,
"cds_length": 834,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945352.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.347G>C",
"hgvs_p": "p.Arg116Thr",
"transcript": "ENST00000893181.1",
"protein_id": "ENSP00000563240.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 237,
"cds_start": 347,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893181.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.347G>C",
"hgvs_p": "p.Arg116Thr",
"transcript": "ENST00000893182.1",
"protein_id": "ENSP00000563241.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 233,
"cds_start": 347,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893182.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"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": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.80G>C",
"hgvs_p": "p.Arg27Thr",
"transcript": "NM_001318845.1",
"protein_id": "NP_001305774.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 189,
"cds_start": 80,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318845.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.347G>C",
"hgvs_p": "p.Arg116Thr",
"transcript": "ENST00000945355.1",
"protein_id": "ENSP00000615414.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 168,
"cds_start": 347,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945355.1"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.347G>C",
"hgvs_p": "p.Arg116Thr",
"transcript": "NM_001318848.2",
"protein_id": "NP_001305777.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 151,
"cds_start": 347,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318848.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.*58G>C",
"hgvs_p": null,
"transcript": "NM_001318847.2",
"protein_id": "NP_001305776.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 116,
"cds_start": null,
"cds_end": null,
"cds_length": 351,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318847.2"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "CNPY3-GNMT",
"gene_hgnc_id": null,
"hgvs_c": "c.151+5924G>C",
"hgvs_p": null,
"transcript": "NM_001318857.2",
"protein_id": "NP_001305786.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 234,
"cds_start": null,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318857.2"
},
{
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CNPY3-GNMT",
"gene_hgnc_id": null,
"hgvs_c": "c.8+5924G>C",
"hgvs_p": null,
"transcript": "NM_001318856.2",
"protein_id": "NP_001305785.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 229,
"cds_start": null,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318856.2"
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.217-2072G>C",
"hgvs_p": null,
"transcript": "ENST00000945353.1",
"protein_id": "ENSP00000615412.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 226,
"cds_start": null,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945353.1"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "CNPY3-GNMT",
"gene_hgnc_id": null,
"hgvs_c": "c.151+5924G>C",
"hgvs_p": null,
"transcript": "NM_001318858.2",
"protein_id": "NP_001305787.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": null,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318858.2"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "c.152-2923G>C",
"hgvs_p": null,
"transcript": "ENST00000924678.1",
"protein_id": "ENSP00000594737.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 124,
"cds_start": null,
"cds_end": null,
"cds_length": 375,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924678.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNPY3",
"gene_hgnc_id": 11968,
"hgvs_c": "n.850G>C",
"hgvs_p": null,
"transcript": "NR_134880.1",
"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": "NR_134880.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
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},
{
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"feature": "NR_134882.1"
},
{
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"biotype": "pseudogene",
"feature": "NR_134885.2"
},
{
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"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
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"exon_count": 2,
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"gene_symbol": "CNPY3",
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"feature": "NR_134886.2"
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{
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"gene_symbol": "CNPY3",
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"feature": "NR_134888.1"
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{
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],
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"gene_symbol": "CNPY3-GNMT",
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"transcript": "NR_134890.2",
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"feature": "NR_134890.2"
},
{
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"intron_variant"
],
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"gene_symbol": "CNPY3-GNMT",
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"biotype": "pseudogene",
"feature": "NR_134891.2"
},
{
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"strand": true,
"consequences": [
"intron_variant"
],
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"gene_symbol": "CNPY3-GNMT",
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"hgvs_c": "n.242+5924G>C",
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"biotype": "pseudogene",
"feature": "NR_134892.2"
}
],
"gene_symbol": "CNPY3",
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"dbsnp": null,
"frequency_reference_population": 6.854094e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.85409e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
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"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6243304014205933,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.607,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.996,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.951,
"phylop100way_prediction": "Pathogenic",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001318842.1",
"gene_symbol": "CNPY3",
"hgnc_id": 11968,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.446G>C",
"hgvs_p": "p.Arg149Thr"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001318857.2",
"gene_symbol": "CNPY3-GNMT",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.151+5924G>C",
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}
],
"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
}