chr6-31277757-A-G

Position:

• chr6-31277757-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP8P1	ENST00000494673.1	n.2186A>G		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.0952

Gnomad4 AMR exome AF: 0.0848

Gnomad4 ASJ exome AF: 0.302

Gnomad4 EAS exome AF: 0.0292

Gnomad4 SAS exome AF: 0.181

Gnomad4 FIN exome AF: 0.0931

Gnomad4 NFE exome AF: 0.127

Gnomad4 OTH exome AF: 0.141

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

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.0539

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0999

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.138

Alfa AF: 0.129 Hom.: 229

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10456057; hg19: chr6-31245534;