← Back to variant description
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: 12-112488439-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=112488439&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 112488439,
"ref": "G",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "NM_001330437.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1380-4G>T",
"hgvs_p": null,
"transcript": "NM_002834.5",
"protein_id": "NP_002825.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 593,
"cds_start": null,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000351677.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002834.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1380-4G>T",
"hgvs_p": null,
"transcript": "ENST00000351677.7",
"protein_id": "ENSP00000340944.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 593,
"cds_start": null,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002834.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000351677.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1392-4G>T",
"hgvs_p": null,
"transcript": "ENST00000635625.1",
"protein_id": "ENSP00000489597.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 597,
"cds_start": null,
"cds_end": null,
"cds_length": 1794,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635625.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.393-4G>T",
"hgvs_p": null,
"transcript": "ENST00000635652.1",
"protein_id": "ENSP00000489541.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 195,
"cds_start": null,
"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": "ENST00000635652.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1380-4G>T",
"hgvs_p": null,
"transcript": "ENST00000690210.1",
"protein_id": "ENSP00000509272.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 671,
"cds_start": null,
"cds_end": null,
"cds_length": 2016,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000690210.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1392-4G>T",
"hgvs_p": null,
"transcript": "NM_001330437.2",
"protein_id": "NP_001317366.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 597,
"cds_start": null,
"cds_end": null,
"cds_length": 1794,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330437.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1389-4G>T",
"hgvs_p": null,
"transcript": "ENST00000882517.1",
"protein_id": "ENSP00000552576.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 596,
"cds_start": null,
"cds_end": null,
"cds_length": 1791,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882517.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1377-4G>T",
"hgvs_p": null,
"transcript": "NM_001374625.1",
"protein_id": "NP_001361554.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 592,
"cds_start": null,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374625.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1377-4G>T",
"hgvs_p": null,
"transcript": "ENST00000882515.1",
"protein_id": "ENSP00000552574.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 592,
"cds_start": null,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882515.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1380-4G>T",
"hgvs_p": null,
"transcript": "ENST00000639857.2",
"protein_id": "ENSP00000491593.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": null,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000639857.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1278-4G>T",
"hgvs_p": null,
"transcript": "ENST00000882516.1",
"protein_id": "ENSP00000552575.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 559,
"cds_start": null,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882516.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1269-4G>T",
"hgvs_p": null,
"transcript": "ENST00000914890.1",
"protein_id": "ENSP00000584949.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 556,
"cds_start": null,
"cds_end": null,
"cds_length": 1671,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914890.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1266-4G>T",
"hgvs_p": null,
"transcript": "ENST00000687906.1",
"protein_id": "ENSP00000509536.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 555,
"cds_start": null,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000687906.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1263-4G>T",
"hgvs_p": null,
"transcript": "ENST00000971611.1",
"protein_id": "ENSP00000641670.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 554,
"cds_start": null,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971611.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1257-4G>T",
"hgvs_p": null,
"transcript": "ENST00000882518.1",
"protein_id": "ENSP00000552577.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 552,
"cds_start": null,
"cds_end": null,
"cds_length": 1659,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882518.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1062-4G>T",
"hgvs_p": null,
"transcript": "ENST00000971614.1",
"protein_id": "ENSP00000641673.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 487,
"cds_start": null,
"cds_end": null,
"cds_length": 1464,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971614.1"
},
{
"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": 13,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1224+6234G>T",
"hgvs_p": null,
"transcript": "ENST00000688597.1",
"protein_id": "ENSP00000510628.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 468,
"cds_start": null,
"cds_end": null,
"cds_length": 1407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000688597.1"
},
{
"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": 13,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1221+6234G>T",
"hgvs_p": null,
"transcript": "ENST00000914889.1",
"protein_id": "ENSP00000584948.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 467,
"cds_start": null,
"cds_end": null,
"cds_length": 1404,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914889.1"
},
{
"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": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1110+6234G>T",
"hgvs_p": null,
"transcript": "ENST00000971615.1",
"protein_id": "ENSP00000641674.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 430,
"cds_start": null,
"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": "ENST00000971615.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.630-4G>T",
"hgvs_p": null,
"transcript": "ENST00000971612.1",
"protein_id": "ENSP00000641671.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 343,
"cds_start": null,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971612.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.588-4G>T",
"hgvs_p": null,
"transcript": "ENST00000971613.1",
"protein_id": "ENSP00000641672.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 329,
"cds_start": null,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971613.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.1389-4G>T",
"hgvs_p": null,
"transcript": "XM_011538613.3",
"protein_id": "XP_011536915.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 596,
"cds_start": null,
"cds_end": null,
"cds_length": 1791,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538613.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.41G>T",
"hgvs_p": null,
"transcript": "ENST00000687624.1",
"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": "retained_intron",
"feature": "ENST00000687624.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.620G>T",
"hgvs_p": null,
"transcript": "ENST00000688701.1",
"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": "retained_intron",
"feature": "ENST00000688701.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.1380-4G>T",
"hgvs_p": null,
"transcript": "ENST00000685487.1",
"protein_id": "ENSP00000508503.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000685487.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.589-4G>T",
"hgvs_p": null,
"transcript": "ENST00000690472.1",
"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": "ENST00000690472.1"
},
{
"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": 15,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.1380-585G>T",
"hgvs_p": null,
"transcript": "ENST00000692624.1",
"protein_id": "ENSP00000508953.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000692624.1"
}
],
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"dbsnp": "rs750640531",
"frequency_reference_population": 0.000004969759,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000343016,
"gnomad_genomes_af": 0.0000197265,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.717,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000768534154971867,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2_Supporting",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2_Supporting"
],
"verdict": "Benign",
"transcript": "NM_001330437.2",
"gene_symbol": "PTPN11",
"hgnc_id": 9644,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1392-4G>T",
"hgvs_p": null
}
],
"clinvar_disease": "RASopathy,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not specified|RASopathy",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}