chr6-31275612-C-A

Position:

• chr6-31275612-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494673.1(USP8P1):​n.41C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 457,708 control chromosomes in the GnomAD database, including 43,788 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 0.44 (14776 hom., cov: 32)
  • Exomes 𝑓: 0.42 (29012 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

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=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP8P1	ENST00000494673.1	n.41C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66846 AN: 151816 Hom.: 14762 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.411

GnomAD4 exome AF: 0.423 AC: 129431 AN: 305772 Hom.: 29012 Cov.: 0 AF XY: 0.414 AC XY: 68475 AN XY: 165302

Gnomad4 AFR exome AF: 0.401

Gnomad4 AMR exome AF: 0.331

Gnomad4 ASJ exome AF: 0.355

Gnomad4 EAS exome AF: 0.362

Gnomad4 SAS exome AF: 0.352

Gnomad4 FIN exome AF: 0.432

Gnomad4 NFE exome AF: 0.455

Gnomad4 OTH exome AF: 0.438

GnomAD4 genome AF: 0.440 AC: 66888 AN: 151936 Hom.: 14776 Cov.: 32 AF XY: 0.435 AC XY: 32342 AN XY: 74282

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.410

Alfa AF: 0.458 Hom.: 1493

Bravo AF: 0.441

Asia WGS AF: 0.478 AC: 1662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	9.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132485; hg19: chr6-31243389;