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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: 18-12817329-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=12817329&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 12817329,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_002828.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.532A>G",
"hgvs_p": "p.Thr178Ala",
"transcript": "NM_002828.4",
"protein_id": "NP_002819.2",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 415,
"cds_start": 532,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000309660.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002828.4"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.532A>G",
"hgvs_p": "p.Thr178Ala",
"transcript": "ENST00000309660.10",
"protein_id": "ENSP00000311857.3",
"transcript_support_level": 1,
"aa_start": 178,
"aa_end": null,
"aa_length": 415,
"cds_start": 532,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002828.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000309660.10"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.601A>G",
"hgvs_p": "p.Thr201Ala",
"transcript": "ENST00000591115.5",
"protein_id": "ENSP00000466936.1",
"transcript_support_level": 1,
"aa_start": 201,
"aa_end": null,
"aa_length": 410,
"cds_start": 601,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000591115.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.532A>G",
"hgvs_p": "p.Thr178Ala",
"transcript": "ENST00000327283.7",
"protein_id": "ENSP00000320298.3",
"transcript_support_level": 1,
"aa_start": 178,
"aa_end": null,
"aa_length": 387,
"cds_start": 532,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000327283.7"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.532A>G",
"hgvs_p": "p.Thr178Ala",
"transcript": "ENST00000353319.8",
"protein_id": "ENSP00000320546.3",
"transcript_support_level": 1,
"aa_start": 178,
"aa_end": null,
"aa_length": 353,
"cds_start": 532,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000353319.8"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.601A>G",
"hgvs_p": "p.Thr201Ala",
"transcript": "ENST00000907074.1",
"protein_id": "ENSP00000577133.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 438,
"cds_start": 601,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907074.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.601A>G",
"hgvs_p": "p.Thr201Ala",
"transcript": "NM_001207013.2",
"protein_id": "NP_001193942.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 410,
"cds_start": 601,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001207013.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.532A>G",
"hgvs_p": "p.Thr178Ala",
"transcript": "NM_080422.3",
"protein_id": "NP_536347.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 387,
"cds_start": 532,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080422.3"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.445A>G",
"hgvs_p": "p.Thr149Ala",
"transcript": "NM_001308287.1",
"protein_id": "NP_001295216.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 386,
"cds_start": 445,
"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": "NM_001308287.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.445A>G",
"hgvs_p": "p.Thr149Ala",
"transcript": "ENST00000591497.5",
"protein_id": "ENSP00000467823.1",
"transcript_support_level": 5,
"aa_start": 149,
"aa_end": null,
"aa_length": 386,
"cds_start": 445,
"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": "ENST00000591497.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.397A>G",
"hgvs_p": "p.Thr133Ala",
"transcript": "ENST00000932005.1",
"protein_id": "ENSP00000602064.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 370,
"cds_start": 397,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932005.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.532A>G",
"hgvs_p": "p.Thr178Ala",
"transcript": "NM_080423.3",
"protein_id": "NP_536348.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 353,
"cds_start": 532,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080423.3"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.235A>G",
"hgvs_p": "p.Thr79Ala",
"transcript": "ENST00000645191.1",
"protein_id": "ENSP00000493693.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 316,
"cds_start": 235,
"cds_end": null,
"cds_length": 951,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000645191.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.235A>G",
"hgvs_p": "p.Thr79Ala",
"transcript": "ENST00000646492.1",
"protein_id": "ENSP00000496181.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 316,
"cds_start": 235,
"cds_end": null,
"cds_length": 951,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000646492.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.853A>G",
"hgvs_p": "p.Thr285Ala",
"transcript": "XM_047437695.1",
"protein_id": "XP_047293651.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 494,
"cds_start": 853,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437695.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.784A>G",
"hgvs_p": "p.Thr262Ala",
"transcript": "XM_047437696.1",
"protein_id": "XP_047293652.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 481,
"cds_start": 784,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437696.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.784A>G",
"hgvs_p": "p.Thr262Ala",
"transcript": "XM_024451229.2",
"protein_id": "XP_024306997.2",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 471,
"cds_start": 784,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451229.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.532A>G",
"hgvs_p": "p.Thr178Ala",
"transcript": "XM_017025884.2",
"protein_id": "XP_016881373.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 397,
"cds_start": 532,
"cds_end": null,
"cds_length": 1194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025884.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.445A>G",
"hgvs_p": "p.Thr149Ala",
"transcript": "XM_047437697.1",
"protein_id": "XP_047293653.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 358,
"cds_start": 445,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437697.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.397A>G",
"hgvs_p": "p.Thr133Ala",
"transcript": "XM_024451228.2",
"protein_id": "XP_024306996.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 342,
"cds_start": 397,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451228.2"
},
{
"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": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.495+8481A>G",
"hgvs_p": null,
"transcript": "ENST00000907073.1",
"protein_id": "ENSP00000577132.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 294,
"cds_start": null,
"cds_end": null,
"cds_length": 885,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907073.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.70-15178A>G",
"hgvs_p": null,
"transcript": "ENST00000932006.1",
"protein_id": "ENSP00000602065.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 152,
"cds_start": null,
"cds_end": null,
"cds_length": 459,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932006.1"
},
{
"aa_ref": null,
"aa_alt": null,
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},
{
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"consequences": [
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],
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"biotype": "pseudogene",
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{
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"protein_coding": false,
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"feature": "ENST00000589216.1"
},
{
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{
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"strand": false,
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],
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{
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"protein_coding": false,
"strand": false,
"consequences": [
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],
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{
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{
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],
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"gene_symbol": "PTPN2",
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{
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"strand": false,
"consequences": [
"intron_variant"
],
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"gene_symbol": "PTPN2",
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"hgvs_c": "n.496-64A>G",
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"transcript": "ENST00000592776.1",
"protein_id": "ENSP00000468155.1",
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000592776.1"
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],
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"dbsnp": "rs527692021",
"frequency_reference_population": 0.0000055768164,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000478915,
"gnomad_genomes_af": 0.0000131418,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8402500152587891,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.864,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6411,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.942,
"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": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002828.4",
"gene_symbol": "PTPN2",
"hgnc_id": 9650,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.532A>G",
"hgvs_p": "p.Thr178Ala"
}
],
"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
}