← 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: 2-55647421-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=55647421&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PNPT1",
"hgnc_id": 23166,
"hgvs_c": "c.1528G>C",
"hgvs_p": "p.Ala510Pro",
"inheritance_mode": "AD,AR,Unknown",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_033109.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PP3_Strong,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 44,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9953,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.22,
"chr": "2",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Combined oxidative phosphorylation defect type 13,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9574368596076965,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 783,
"aa_ref": "A",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4549,
"cdna_start": 1549,
"cds_end": null,
"cds_length": 2352,
"cds_start": 1528,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_033109.5",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1528G>C",
"hgvs_p": "p.Ala510Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000447944.7",
"protein_coding": true,
"protein_id": "NP_149100.2",
"strand": false,
"transcript": "NM_033109.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 783,
"aa_ref": "A",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4549,
"cdna_start": 1549,
"cds_end": null,
"cds_length": 2352,
"cds_start": 1528,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000447944.7",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1528G>C",
"hgvs_p": "p.Ala510Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_033109.5",
"protein_coding": true,
"protein_id": "ENSP00000400646.2",
"strand": false,
"transcript": "ENST00000447944.7",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 789,
"aa_ref": "A",
"aa_start": 516,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2644,
"cdna_start": 1566,
"cds_end": null,
"cds_length": 2370,
"cds_start": 1546,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000917025.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1546G>C",
"hgvs_p": "p.Ala516Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587084.1",
"strand": false,
"transcript": "ENST00000917025.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 782,
"aa_ref": "A",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2661,
"cdna_start": 1540,
"cds_end": null,
"cds_length": 2349,
"cds_start": 1528,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000867135.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1528G>C",
"hgvs_p": "p.Ala510Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537194.1",
"strand": false,
"transcript": "ENST00000867135.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 782,
"aa_ref": "A",
"aa_start": 509,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4517,
"cdna_start": 1546,
"cds_end": null,
"cds_length": 2349,
"cds_start": 1525,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000917023.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1525G>C",
"hgvs_p": "p.Ala509Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587082.1",
"strand": false,
"transcript": "ENST00000917023.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 781,
"aa_ref": "A",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2604,
"cdna_start": 1540,
"cds_end": null,
"cds_length": 2346,
"cds_start": 1528,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000949803.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1528G>C",
"hgvs_p": "p.Ala510Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619862.1",
"strand": false,
"transcript": "ENST00000949803.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 780,
"aa_ref": "A",
"aa_start": 507,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3262,
"cdna_start": 1533,
"cds_end": null,
"cds_length": 2343,
"cds_start": 1519,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000949801.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1519G>C",
"hgvs_p": "p.Ala507Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619860.1",
"strand": false,
"transcript": "ENST00000949801.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 767,
"aa_ref": "A",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2572,
"cdna_start": 1542,
"cds_end": null,
"cds_length": 2304,
"cds_start": 1528,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000867137.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1528G>C",
"hgvs_p": "p.Ala510Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537196.1",
"strand": false,
"transcript": "ENST00000867137.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 767,
"aa_ref": "A",
"aa_start": 494,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4472,
"cdna_start": 1501,
"cds_end": null,
"cds_length": 2304,
"cds_start": 1480,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000917022.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1480G>C",
"hgvs_p": "p.Ala494Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587081.1",
"strand": false,
"transcript": "ENST00000917022.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 765,
"aa_ref": "A",
"aa_start": 492,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3210,
"cdna_start": 1481,
"cds_end": null,
"cds_length": 2298,
"cds_start": 1474,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000867134.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1474G>C",
"hgvs_p": "p.Ala492Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537193.1",
"strand": false,
"transcript": "ENST00000867134.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 760,
"aa_ref": "A",
"aa_start": 487,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2539,
"cdna_start": 1469,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1459,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000949804.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1459G>C",
"hgvs_p": "p.Ala487Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619863.1",
"strand": false,
"transcript": "ENST00000949804.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 759,
"aa_ref": "A",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3436,
"cdna_start": 1544,
"cds_end": null,
"cds_length": 2280,
"cds_start": 1528,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000917024.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1528G>C",
"hgvs_p": "p.Ala510Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587083.1",
"strand": false,
"transcript": "ENST00000917024.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 758,
"aa_ref": "A",
"aa_start": 485,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2552,
"cdna_start": 1474,
"cds_end": null,
"cds_length": 2277,
"cds_start": 1453,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000867136.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1453G>C",
"hgvs_p": "p.Ala485Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537195.1",
"strand": false,
"transcript": "ENST00000867136.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 755,
"aa_ref": "A",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3191,
"cdna_start": 1546,
"cds_end": null,
"cds_length": 2268,
"cds_start": 1528,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000867132.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1528G>C",
"hgvs_p": "p.Ala510Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537192.1",
"strand": false,
"transcript": "ENST00000867132.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 747,
"aa_ref": "A",
"aa_start": 474,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2859,
"cdna_start": 1432,
"cds_end": null,
"cds_length": 2244,
"cds_start": 1420,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000949802.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1420G>C",
"hgvs_p": "p.Ala474Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619861.1",
"strand": false,
"transcript": "ENST00000949802.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 745,
"aa_ref": "A",
"aa_start": 472,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4388,
"cdna_start": 1426,
"cds_end": null,
"cds_length": 2238,
"cds_start": 1414,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000949800.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1414G>C",
"hgvs_p": "p.Ala472Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619859.1",
"strand": false,
"transcript": "ENST00000949800.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 725,
"aa_ref": "A",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2328,
"cdna_start": 1371,
"cds_end": null,
"cds_length": 2178,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000917027.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1354G>C",
"hgvs_p": "p.Ala452Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587086.1",
"strand": false,
"transcript": "ENST00000917027.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 703,
"aa_ref": "A",
"aa_start": 430,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4545,
"cdna_start": 1545,
"cds_end": null,
"cds_length": 2112,
"cds_start": 1288,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_005264629.3",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1288G>C",
"hgvs_p": "p.Ala430Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005264686.1",
"strand": false,
"transcript": "XM_005264629.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 703,
"aa_ref": "A",
"aa_start": 430,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4488,
"cdna_start": 1488,
"cds_end": null,
"cds_length": 2112,
"cds_start": 1288,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_017005172.2",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1288G>C",
"hgvs_p": "p.Ala430Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016860661.1",
"strand": false,
"transcript": "XM_017005172.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 504,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1744,
"cdna_start": null,
"cds_end": null,
"cds_length": 1515,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_047446161.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.*60G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047302117.1",
"strand": false,
"transcript": "XM_047446161.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 677,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2188,
"cdna_start": null,
"cds_end": null,
"cds_length": 2034,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000917026.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.1285-935G>C",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587085.1",
"strand": false,
"transcript": "ENST00000917026.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 684,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000867138.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "c.223-9822G>C",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537197.1",
"strand": false,
"transcript": "ENST00000867138.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3596,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 27,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000260604.8",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "n.*1083G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000260604.4",
"strand": false,
"transcript": "ENST00000260604.8",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3308,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 29,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000415374.5",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "n.1528G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000393953.1",
"strand": false,
"transcript": "ENST00000415374.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 555,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000415489.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "n.*117G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000411057.1",
"strand": false,
"transcript": "ENST00000415489.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3596,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 27,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000260604.8",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "n.*1083G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000260604.4",
"strand": false,
"transcript": "ENST00000260604.8",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 555,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000415489.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "n.*117G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000411057.1",
"strand": false,
"transcript": "ENST00000415489.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1281,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000481066.1",
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"hgvs_c": "n.-39G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000481066.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs879255657",
"effect": "missense_variant",
"frequency_reference_population": 0.000027350325,
"gene_hgnc_id": 23166,
"gene_symbol": "PNPT1",
"gnomad_exomes_ac": 42,
"gnomad_exomes_af": 0.0000288326,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131518,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Combined oxidative phosphorylation defect type 13|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.364,
"pos": 55647421,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.629,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.11999999731779099,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.12,
"transcript": "NM_033109.5"
}
]
}