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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: 17-45453712-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=45453712&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 45453712,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000430334.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"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": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.2140C>T",
"hgvs_p": "p.Arg714Cys",
"transcript": "NM_014798.3",
"protein_id": "NP_055613.1",
"transcript_support_level": null,
"aa_start": 714,
"aa_end": null,
"aa_length": 1056,
"cds_start": 2140,
"cds_end": null,
"cds_length": 3171,
"cdna_start": 2251,
"cdna_end": null,
"cdna_length": 5240,
"mane_select": "ENST00000430334.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"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": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.2140C>T",
"hgvs_p": "p.Arg714Cys",
"transcript": "ENST00000430334.8",
"protein_id": "ENSP00000389913.3",
"transcript_support_level": 1,
"aa_start": 714,
"aa_end": null,
"aa_length": 1056,
"cds_start": 2140,
"cds_end": null,
"cds_length": 3171,
"cdna_start": 2251,
"cdna_end": null,
"cdna_length": 5240,
"mane_select": "NM_014798.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.1611C>T",
"hgvs_p": null,
"transcript": "ENST00000580205.1",
"protein_id": null,
"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": 2385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.*747C>T",
"hgvs_p": null,
"transcript": "ENST00000581448.5",
"protein_id": "ENSP00000462160.1",
"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": 3292,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.*747C>T",
"hgvs_p": null,
"transcript": "ENST00000581448.5",
"protein_id": "ENSP00000462160.1",
"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": 3292,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"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": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.2140C>T",
"hgvs_p": "p.Arg714Cys",
"transcript": "ENST00000446609.7",
"protein_id": "ENSP00000394344.3",
"transcript_support_level": 5,
"aa_start": 714,
"aa_end": null,
"aa_length": 1056,
"cds_start": 2140,
"cds_end": null,
"cds_length": 3171,
"cdna_start": 2312,
"cdna_end": null,
"cdna_length": 4299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.2140C>T",
"hgvs_p": "p.Arg714Cys",
"transcript": "NM_001352825.2",
"protein_id": "NP_001339754.1",
"transcript_support_level": null,
"aa_start": 714,
"aa_end": null,
"aa_length": 853,
"cds_start": 2140,
"cds_end": null,
"cds_length": 2562,
"cdna_start": 2251,
"cdna_end": null,
"cdna_length": 3029,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.2140C>T",
"hgvs_p": "p.Arg714Cys",
"transcript": "ENST00000700125.1",
"protein_id": "ENSP00000514814.1",
"transcript_support_level": null,
"aa_start": 714,
"aa_end": null,
"aa_length": 853,
"cds_start": 2140,
"cds_end": null,
"cds_length": 2562,
"cdna_start": 2288,
"cdna_end": null,
"cdna_length": 3075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"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": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.2140C>T",
"hgvs_p": "p.Arg714Cys",
"transcript": "XM_017025451.2",
"protein_id": "XP_016880940.1",
"transcript_support_level": null,
"aa_start": 714,
"aa_end": null,
"aa_length": 1056,
"cds_start": 2140,
"cds_end": null,
"cds_length": 3171,
"cdna_start": 3666,
"cdna_end": null,
"cdna_length": 6655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.2140C>T",
"hgvs_p": "p.Arg714Cys",
"transcript": "XM_047437188.1",
"protein_id": "XP_047293144.1",
"transcript_support_level": null,
"aa_start": 714,
"aa_end": null,
"aa_length": 1056,
"cds_start": 2140,
"cds_end": null,
"cds_length": 3171,
"cdna_start": 3666,
"cdna_end": null,
"cdna_length": 4873,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"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": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.1987C>T",
"hgvs_p": "p.Arg663Cys",
"transcript": "XM_011525525.1",
"protein_id": "XP_011523827.1",
"transcript_support_level": null,
"aa_start": 663,
"aa_end": null,
"aa_length": 1005,
"cds_start": 1987,
"cds_end": null,
"cds_length": 3018,
"cdna_start": 2068,
"cdna_end": null,
"cdna_length": 5057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"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": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.2140C>T",
"hgvs_p": "p.Arg714Cys",
"transcript": "XM_047437189.1",
"protein_id": "XP_047293145.1",
"transcript_support_level": null,
"aa_start": 714,
"aa_end": null,
"aa_length": 994,
"cds_start": 2140,
"cds_end": null,
"cds_length": 2985,
"cdna_start": 3666,
"cdna_end": null,
"cdna_length": 4614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.1939C>T",
"hgvs_p": "p.Arg647Cys",
"transcript": "XM_047437190.1",
"protein_id": "XP_047293146.1",
"transcript_support_level": null,
"aa_start": 647,
"aa_end": null,
"aa_length": 989,
"cds_start": 1939,
"cds_end": null,
"cds_length": 2970,
"cdna_start": 3465,
"cdna_end": null,
"cdna_length": 6454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"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": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.1873C>T",
"hgvs_p": "p.Arg625Cys",
"transcript": "XM_017025452.2",
"protein_id": "XP_016880941.1",
"transcript_support_level": null,
"aa_start": 625,
"aa_end": null,
"aa_length": 967,
"cds_start": 1873,
"cds_end": null,
"cds_length": 2904,
"cdna_start": 3418,
"cdna_end": null,
"cdna_length": 6407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"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": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.1987C>T",
"hgvs_p": "p.Arg663Cys",
"transcript": "XM_047437191.1",
"protein_id": "XP_047293147.1",
"transcript_support_level": null,
"aa_start": 663,
"aa_end": null,
"aa_length": 943,
"cds_start": 1987,
"cds_end": null,
"cds_length": 2832,
"cdna_start": 2068,
"cdna_end": null,
"cdna_length": 3016,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.1750C>T",
"hgvs_p": "p.Arg584Cys",
"transcript": "XM_006722201.5",
"protein_id": "XP_006722264.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 926,
"cds_start": 1750,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 2094,
"cdna_end": null,
"cdna_length": 5083,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.1750C>T",
"hgvs_p": "p.Arg584Cys",
"transcript": "XM_047437192.1",
"protein_id": "XP_047293148.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 926,
"cds_start": 1750,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 1870,
"cdna_end": null,
"cdna_length": 4859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.577C>T",
"hgvs_p": "p.Arg193Cys",
"transcript": "XM_011525528.3",
"protein_id": "XP_011523830.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 535,
"cds_start": 577,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 627,
"cdna_end": null,
"cdna_length": 3616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.*1700C>T",
"hgvs_p": null,
"transcript": "ENST00000579197.5",
"protein_id": "ENSP00000462282.1",
"transcript_support_level": 2,
"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": 4995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.*1717C>T",
"hgvs_p": null,
"transcript": "ENST00000700123.1",
"protein_id": "ENSP00000514812.1",
"transcript_support_level": null,
"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": 4145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.*1882C>T",
"hgvs_p": null,
"transcript": "ENST00000700124.1",
"protein_id": "ENSP00000514813.1",
"transcript_support_level": null,
"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": 4457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.2011C>T",
"hgvs_p": null,
"transcript": "ENST00000700126.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2479,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.2268C>T",
"hgvs_p": null,
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},
{
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},
{
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},
{
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},
{
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},
{
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],
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}
],
"gene_symbol": "PLEKHM1",
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"dbsnp": "rs559224144",
"frequency_reference_population": 0.000001858918,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
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"gnomad_genomes_af": 0.00000657073,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9370237588882446,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.351,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1236,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.508,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000430334.8",
"gene_symbol": "PLEKHM1",
"hgnc_id": 29017,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.2140C>T",
"hgvs_p": "p.Arg714Cys"
},
{
"score": 5,
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"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000433601.1",
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"effects": [
"intron_variant"
],
"inheritance_mode": "",
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}
],
"clinvar_disease": " autosomal dominant 3,Osteopetrosis",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Osteopetrosis, autosomal dominant 3",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}