rs2524074

Positions:

• chr6-31276244-G-A

Variant summary

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

The ENST00000494673.1(USP8P1):​n.673G>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 0.73 in 742,770 control chromosomes in the GnomAD database, including 200,532 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 0.75 (43214 hom., cov: 31)
  • Exomes 𝑓: 0.72 (157318 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

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=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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.673G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114167 AN: 152038 Hom.: 43180 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.783

GnomAD4 exome AF: 0.725 AC: 427976 AN: 590614 Hom.: 157318 Cov.: 5 AF XY: 0.727 AC XY: 233607 AN XY: 321336

Gnomad4 AFR exome AF: 0.799

Gnomad4 AMR exome AF: 0.760

Gnomad4 ASJ exome AF: 0.865

Gnomad4 EAS exome AF: 0.853

Gnomad4 SAS exome AF: 0.770

Gnomad4 FIN exome AF: 0.730

Gnomad4 NFE exome AF: 0.686

Gnomad4 OTH exome AF: 0.728

GnomAD4 genome AF: 0.751 AC: 114249 AN: 152156 Hom.: 43214 Cov.: 31 AF XY: 0.755 AC XY: 56190 AN XY: 74402

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.783

Alfa AF: 0.729 Hom.: 3765

Bravo AF: 0.755

Asia WGS AF: 0.801 AC: 2786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	12
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524074; hg19: chr6-31244021;