ENST00000494673.1:n.2186A>G

Variant names:

• chr6-31277757-A-G
• rs10456057
• ENST00000494673.1:n.2186A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494673.1(USP8P1):​n.2186A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.128 in 1,601,346 control chromosomes in the GnomAD database, including 14,836 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.13 (1309 hom., cov: 33)
  • Exomes 𝑓: 0.13 (13527 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.11
• Publications: 15 publications found

Genes affected

USP8P1 (HGNC:13987): (USP8 pseudogene 1)

ENSG00000298396 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP8P1		n.31277757A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP8P1	ENST00000494673.1	n.2186A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298396	ENST00000755297.1	n.32+6651A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19054 AN: 152104 Hom.: 1309 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.140

GnomAD4 exome AF: 0.128 AC: 186004 AN: 1449124 Hom.: 13527 Cov.: 35 AF XY: 0.132 AC XY: 95126 AN XY: 721676

African (AFR) AF: 0.0952 AC: 3162 AN: 33214

American (AMR) AF: 0.0848 AC: 3790 AN: 44698

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 7879 AN: 26050

East Asian (EAS) AF: 0.0292 AC: 1156 AN: 39638

South Asian (SAS) AF: 0.181 AC: 15590 AN: 85978

European-Finnish (FIN) AF: 0.0931 AC: 4968 AN: 53356

Middle Eastern (MID) AF: 0.230 AC: 1319 AN: 5742

European-Non Finnish (NFE) AF: 0.127 AC: 139686 AN: 1100486

Other (OTH) AF: 0.141 AC: 8454 AN: 59962

GnomAD4 genome AF: 0.125 AC: 19058 AN: 152222 Hom.: 1309 Cov.: 33 AF XY: 0.125 AC XY: 9338 AN XY: 74416

African (AFR) AF: 0.106 AC: 4415 AN: 41534

American (AMR) AF: 0.110 AC: 1683 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3470

East Asian (EAS) AF: 0.0539 AC: 279 AN: 5176

South Asian (SAS) AF: 0.165 AC: 796 AN: 4830

European-Finnish (FIN) AF: 0.0999 AC: 1059 AN: 10602

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.135 AC: 9192 AN: 67996

Other (OTH) AF: 0.138 AC: 291 AN: 2114

Alfa AF: 0.127 Hom.: 1982

Bravo AF: 0.125

Asia WGS AF: 0.0930 AC: 326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.56
PhyloP100		4.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10456057; hg19: chr6-31245534;