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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: 11-18733237-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=18733237&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 18733237,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_006906.2",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys",
"transcript": "NM_006906.2",
"protein_id": "NP_008837.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 565,
"cds_start": 1216,
"cds_end": null,
"cds_length": 1698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000358540.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006906.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys",
"transcript": "ENST00000358540.7",
"protein_id": "ENSP00000351342.2",
"transcript_support_level": 1,
"aa_start": 406,
"aa_end": null,
"aa_length": 565,
"cds_start": 1216,
"cds_end": null,
"cds_length": 1698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006906.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358540.7"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Glu382Lys",
"transcript": "ENST00000396168.1",
"protein_id": "ENSP00000379471.1",
"transcript_support_level": 1,
"aa_start": 382,
"aa_end": null,
"aa_length": 541,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1626,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396168.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1291G>A",
"hgvs_p": "p.Glu431Lys",
"transcript": "ENST00000935333.1",
"protein_id": "ENSP00000605392.1",
"transcript_support_level": null,
"aa_start": 431,
"aa_end": null,
"aa_length": 590,
"cds_start": 1291,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935333.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys",
"transcript": "NM_032781.4",
"protein_id": "NP_116170.3",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 565,
"cds_start": 1216,
"cds_end": null,
"cds_length": 1698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032781.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys",
"transcript": "ENST00000856224.1",
"protein_id": "ENSP00000526283.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 565,
"cds_start": 1216,
"cds_end": null,
"cds_length": 1698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856224.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys",
"transcript": "ENST00000856226.1",
"protein_id": "ENSP00000526285.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 552,
"cds_start": 1216,
"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": "ENST00000856226.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Glu382Lys",
"transcript": "NM_001278238.2",
"protein_id": "NP_001265167.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 541,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1626,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278238.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Glu374Lys",
"transcript": "NM_001039970.2",
"protein_id": "NP_001035059.1",
"transcript_support_level": null,
"aa_start": 374,
"aa_end": null,
"aa_length": 533,
"cds_start": 1120,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001039970.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Glu374Lys",
"transcript": "NM_001278236.1",
"protein_id": "NP_001265165.1",
"transcript_support_level": null,
"aa_start": 374,
"aa_end": null,
"aa_length": 533,
"cds_start": 1120,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278236.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Glu374Lys",
"transcript": "ENST00000396170.5",
"protein_id": "ENSP00000379473.1",
"transcript_support_level": 2,
"aa_start": 374,
"aa_end": null,
"aa_length": 533,
"cds_start": 1120,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396170.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Glu374Lys",
"transcript": "ENST00000957011.1",
"protein_id": "ENSP00000627070.1",
"transcript_support_level": null,
"aa_start": 374,
"aa_end": null,
"aa_length": 533,
"cds_start": 1120,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957011.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys",
"transcript": "ENST00000957010.1",
"protein_id": "ENSP00000627069.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 528,
"cds_start": 1216,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957010.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Glu350Lys",
"transcript": "NM_001278239.2",
"protein_id": "NP_001265168.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 509,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278239.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys",
"transcript": "ENST00000957013.1",
"protein_id": "ENSP00000627072.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 493,
"cds_start": 1216,
"cds_end": null,
"cds_length": 1482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957013.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.628G>A",
"hgvs_p": "p.Glu210Lys",
"transcript": "ENST00000477854.5",
"protein_id": "ENSP00000435056.1",
"transcript_support_level": 5,
"aa_start": 210,
"aa_end": null,
"aa_length": 369,
"cds_start": 628,
"cds_end": null,
"cds_length": 1110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000477854.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys",
"transcript": "XM_017018434.3",
"protein_id": "XP_016873923.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 719,
"cds_start": 1216,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018434.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys",
"transcript": "XM_017018435.3",
"protein_id": "XP_016873924.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 719,
"cds_start": 1216,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018435.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Glu382Lys",
"transcript": "XM_017018436.2",
"protein_id": "XP_016873925.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 695,
"cds_start": 1144,
"cds_end": null,
"cds_length": 2088,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018436.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Glu374Lys",
"transcript": "XM_017018437.2",
"protein_id": "XP_016873926.1",
"transcript_support_level": null,
"aa_start": 374,
"aa_end": null,
"aa_length": 687,
"cds_start": 1120,
"cds_end": null,
"cds_length": 2064,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018437.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1099G>A",
"hgvs_p": "p.Glu367Lys",
"transcript": "XM_017018438.3",
"protein_id": "XP_016873927.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 680,
"cds_start": 1099,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018438.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
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{
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"canonical": false,
"protein_coding": true,
"strand": false,
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],
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"intron_rank": 10,
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"transcript": "ENST00000856225.1",
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"biotype": "protein_coding",
"feature": "ENST00000856225.1"
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{
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"protein_coding": true,
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],
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"gene_symbol": "PTPN5",
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"transcript": "ENST00000957012.1",
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"biotype": "protein_coding",
"feature": "ENST00000957012.1"
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{
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"protein_coding": false,
"strand": true,
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"intron_variant"
],
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"gene_symbol": "IGSF22-AS1",
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"biotype": "pseudogene",
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{
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"intron_variant"
],
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"gene_symbol": "IGSF22-AS1",
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"biotype": "pseudogene",
"feature": "NR_186353.1"
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],
"gene_symbol": "PTPN5",
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"dbsnp": "rs139371305",
"frequency_reference_population": 0.00015833159,
"hom_count_reference_population": 2,
"allele_count_reference_population": 255,
"gnomad_exomes_af": 0.000153593,
"gnomad_genomes_af": 0.000203752,
"gnomad_exomes_ac": 224,
"gnomad_genomes_ac": 31,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6951819658279419,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.7919999957084656,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.575,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9516,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.794,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.922485189194405,
"dbscsnv_ada_prediction": "Benign",
"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_006906.2",
"gene_symbol": "PTPN5",
"hgnc_id": 9657,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1216G>A",
"hgvs_p": "p.Glu406Lys"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000527285.1",
"gene_symbol": "IGSF22-AS1",
"hgnc_id": 55511,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.730-7187C>T",
"hgvs_p": null
}
],
"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
}