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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: 3-46579986-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=46579986&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 46579986,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003212.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.374C>T",
"hgvs_p": "p.Pro125Leu",
"transcript": "NM_003212.4",
"protein_id": "NP_003203.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 188,
"cds_start": 374,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000296145.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003212.4"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.374C>T",
"hgvs_p": "p.Pro125Leu",
"transcript": "ENST00000296145.6",
"protein_id": "ENSP00000296145.5",
"transcript_support_level": 1,
"aa_start": 125,
"aa_end": null,
"aa_length": 188,
"cds_start": 374,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003212.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296145.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRC2",
"gene_hgnc_id": 14676,
"hgvs_c": "c.-69G>A",
"hgvs_p": null,
"transcript": "ENST00000296144.3",
"protein_id": "ENSP00000296144.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": null,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296144.3"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Pro193Leu",
"transcript": "ENST00000938312.1",
"protein_id": "ENSP00000608371.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 256,
"cds_start": 578,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938312.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.509C>T",
"hgvs_p": "p.Pro170Leu",
"transcript": "ENST00000938314.1",
"protein_id": "ENSP00000608373.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 233,
"cds_start": 509,
"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": "ENST00000938314.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.401C>T",
"hgvs_p": "p.Pro134Leu",
"transcript": "ENST00000938308.1",
"protein_id": "ENSP00000608367.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 197,
"cds_start": 401,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938308.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu",
"transcript": "ENST00000951684.1",
"protein_id": "ENSP00000621743.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 195,
"cds_start": 395,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951684.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.374C>T",
"hgvs_p": "p.Pro125Leu",
"transcript": "ENST00000863382.1",
"protein_id": "ENSP00000533441.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 188,
"cds_start": 374,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863382.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.374C>T",
"hgvs_p": "p.Pro125Leu",
"transcript": "ENST00000938305.1",
"protein_id": "ENSP00000608364.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 188,
"cds_start": 374,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938305.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.374C>T",
"hgvs_p": "p.Pro125Leu",
"transcript": "ENST00000938306.1",
"protein_id": "ENSP00000608365.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 188,
"cds_start": 374,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938306.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.374C>T",
"hgvs_p": "p.Pro125Leu",
"transcript": "ENST00000938310.1",
"protein_id": "ENSP00000608369.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 188,
"cds_start": 374,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938310.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.326C>T",
"hgvs_p": "p.Pro109Leu",
"transcript": "NM_001174136.2",
"protein_id": "NP_001167607.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 172,
"cds_start": 326,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001174136.2"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.326C>T",
"hgvs_p": "p.Pro109Leu",
"transcript": "ENST00000542931.6",
"protein_id": "ENSP00000446375.1",
"transcript_support_level": 5,
"aa_start": 109,
"aa_end": null,
"aa_length": 172,
"cds_start": 326,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000542931.6"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.317C>T",
"hgvs_p": "p.Pro106Leu",
"transcript": "ENST00000938309.1",
"protein_id": "ENSP00000608368.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 169,
"cds_start": 317,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938309.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.71C>T",
"hgvs_p": "p.Pro24Leu",
"transcript": "ENST00000938313.1",
"protein_id": "ENSP00000608372.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 87,
"cds_start": 71,
"cds_end": null,
"cds_length": 264,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938313.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRC2",
"gene_hgnc_id": 14676,
"hgvs_c": "c.-187G>A",
"hgvs_p": null,
"transcript": "ENST00000938206.1",
"protein_id": "ENSP00000608265.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": null,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938206.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LRRC2",
"gene_hgnc_id": 14676,
"hgvs_c": "c.-20+26823G>A",
"hgvs_p": null,
"transcript": "ENST00000682605.1",
"protein_id": "ENSP00000507018.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": null,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682605.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LRRC2",
"gene_hgnc_id": 14676,
"hgvs_c": "c.-20+13228G>A",
"hgvs_p": null,
"transcript": "ENST00000951503.1",
"protein_id": "ENSP00000621562.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": null,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951503.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LRRC2",
"gene_hgnc_id": 14676,
"hgvs_c": "c.-20+13228G>A",
"hgvs_p": null,
"transcript": "ENST00000951504.1",
"protein_id": "ENSP00000621563.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": null,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951504.1"
},
{
"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": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.316+155C>T",
"hgvs_p": null,
"transcript": "ENST00000938311.1",
"protein_id": "ENSP00000608370.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 144,
"cds_start": null,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938311.1"
},
{
"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": 3,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "c.223+620C>T",
"hgvs_p": null,
"transcript": "ENST00000938307.1",
"protein_id": "ENSP00000608366.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 113,
"cds_start": null,
"cds_end": null,
"cds_length": 342,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938307.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "n.*207C>T",
"hgvs_p": null,
"transcript": "ENST00000459867.1",
"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": "retained_intron",
"feature": "ENST00000459867.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"hgvs_c": "n.*50C>T",
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"transcript": "ENST00000493282.5",
"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": "ENST00000493282.5"
}
],
"gene_symbol": "CRIPTO",
"gene_hgnc_id": 11701,
"dbsnp": "rs121909501",
"frequency_reference_population": 0.00024471598,
"hom_count_reference_population": 0,
"allele_count_reference_population": 395,
"gnomad_exomes_af": 0.000251733,
"gnomad_genomes_af": 0.000177342,
"gnomad_exomes_ac": 368,
"gnomad_genomes_ac": 27,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6600666642189026,
"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": 0.2033,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.192,
"phylop100way_prediction": "Benign",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_003212.4",
"gene_symbol": "CRIPTO",
"hgnc_id": 11701,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.374C>T",
"hgvs_p": "p.Pro125Leu"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000296144.3",
"gene_symbol": "LRRC2",
"hgnc_id": 14676,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-69G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Forebrain defects",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Forebrain defects",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}