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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: 2-58088354-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=58088354&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 58088354,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_006296.7",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "NM_006296.7",
"protein_id": "NP_006287.2",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 508,
"cds_start": 358,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 426,
"cdna_end": null,
"cdna_length": 1773,
"mane_select": "ENST00000340157.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "ENST00000340157.9",
"protein_id": "ENSP00000342381.4",
"transcript_support_level": 1,
"aa_start": 120,
"aa_end": null,
"aa_length": 508,
"cds_start": 358,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 426,
"cdna_end": null,
"cdna_length": 1773,
"mane_select": "NM_006296.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "ENST00000435505.6",
"protein_id": "ENSP00000408002.2",
"transcript_support_level": 1,
"aa_start": 120,
"aa_end": null,
"aa_length": 508,
"cds_start": 358,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 1103,
"cdna_end": null,
"cdna_length": 2446,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.289G>C",
"hgvs_p": "p.Val97Leu",
"transcript": "ENST00000440705.6",
"protein_id": "ENSP00000398323.2",
"transcript_support_level": 1,
"aa_start": 97,
"aa_end": null,
"aa_length": 485,
"cds_start": 289,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 416,
"cdna_end": null,
"cdna_length": 1676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.4G>C",
"hgvs_p": "p.Val2Leu",
"transcript": "ENST00000412104.6",
"protein_id": "ENSP00000404156.3",
"transcript_support_level": 1,
"aa_start": 2,
"aa_end": null,
"aa_length": 390,
"cds_start": 4,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "n.*315G>C",
"hgvs_p": null,
"transcript": "ENST00000432057.2",
"protein_id": "ENSP00000400006.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "n.*315G>C",
"hgvs_p": null,
"transcript": "ENST00000432057.2",
"protein_id": "ENSP00000400006.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "NM_001130480.2",
"protein_id": "NP_001123952.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 508,
"cds_start": 358,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 543,
"cdna_end": null,
"cdna_length": 1939,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "NM_001130481.2",
"protein_id": "NP_001123953.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 508,
"cds_start": 358,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 385,
"cdna_end": null,
"cdna_length": 1781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "NM_001288837.2",
"protein_id": "NP_001275766.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 508,
"cds_start": 358,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 1162,
"cdna_end": null,
"cdna_length": 2509,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.289G>C",
"hgvs_p": "p.Val97Leu",
"transcript": "NM_001130482.2",
"protein_id": "NP_001123954.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 485,
"cds_start": 289,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 489,
"cdna_end": null,
"cdna_length": 1885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "ENST00000648897.1",
"protein_id": "ENSP00000497378.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 397,
"cds_start": 358,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 1297,
"cdna_end": null,
"cdna_length": 2657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "NM_001130483.2",
"protein_id": "NP_001123955.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 396,
"cds_start": 358,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 543,
"cdna_end": null,
"cdna_length": 1988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "NM_001288838.2",
"protein_id": "NP_001275767.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 396,
"cds_start": 358,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1044,
"cdna_end": null,
"cdna_length": 2440,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "ENST00000417641.6",
"protein_id": "ENSP00000402375.2",
"transcript_support_level": 2,
"aa_start": 120,
"aa_end": null,
"aa_length": 396,
"cds_start": 358,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 2381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.4G>C",
"hgvs_p": "p.Val2Leu",
"transcript": "NM_001288836.1",
"protein_id": "NP_001275765.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 390,
"cds_start": 4,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 680,
"cdna_end": null,
"cdna_length": 2076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.4G>C",
"hgvs_p": "p.Val2Leu",
"transcript": "NM_001288839.2",
"protein_id": "NP_001275768.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 390,
"cds_start": 4,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 356,
"cdna_end": null,
"cdna_length": 1703,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "XM_005264540.5",
"protein_id": "XP_005264597.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 508,
"cds_start": 358,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 686,
"cdna_end": null,
"cdna_length": 2082,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "XM_011533092.4",
"protein_id": "XP_011531394.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 508,
"cds_start": 358,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 545,
"cdna_end": null,
"cdna_length": 1941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "XM_006712090.5",
"protein_id": "XP_006712153.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 397,
"cds_start": 358,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 426,
"cdna_end": null,
"cdna_length": 1866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu",
"transcript": "XM_006712091.5",
"protein_id": "XP_006712154.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 396,
"cds_start": 358,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 426,
"cdna_end": null,
"cdna_length": 1871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.4G>C",
"hgvs_p": "p.Val2Leu",
"transcript": "XM_047445745.1",
"protein_id": "XP_047301701.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 390,
"cds_start": 4,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 1594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.4G>C",
"hgvs_p": "p.Val2Leu",
"transcript": "XM_047445747.1",
"protein_id": "XP_047301703.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 390,
"cds_start": 4,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 1597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.4G>C",
"hgvs_p": "p.Val2Leu",
"transcript": "XM_047445748.1",
"protein_id": "XP_047301704.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 390,
"cds_start": 4,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 205,
"cdna_end": null,
"cdna_length": 1601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"dbsnp": "rs1274707992",
"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": 0.8008335828781128,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.467,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7679,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.475,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.06,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006296.7",
"gene_symbol": "VRK2",
"hgnc_id": 12719,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.358G>C",
"hgvs_p": "p.Val120Leu"
}
],
"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
}