rs2524077

Positions:

• chr6-31275826-C-T

Variant summary

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

The ENST00000494673.1(USP8P1):​n.255C>T 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 0.114 in 819,804 control chromosomes in the GnomAD database, including 6,165 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 0.12 (1135 hom., cov: 32)
  • Exomes 𝑓: 0.11 (5030 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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.255C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17865 AN: 152048 Hom.: 1134 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.0514

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.113 AC: 75401 AN: 667638 Hom.: 5030 Cov.: 8 AF XY: 0.109 AC XY: 39170 AN XY: 360684

Gnomad4 AFR exome AF: 0.120

Gnomad4 AMR exome AF: 0.136

Gnomad4 ASJ exome AF: 0.169

Gnomad4 EAS exome AF: 0.0985

Gnomad4 SAS exome AF: 0.0485

Gnomad4 FIN exome AF: 0.0559

Gnomad4 NFE exome AF: 0.127

Gnomad4 OTH exome AF: 0.130

GnomAD4 genome AF: 0.117 AC: 17865 AN: 152166 Hom.: 1135 Cov.: 32 AF XY: 0.112 AC XY: 8354 AN XY: 74380

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0762

Gnomad4 FIN AF: 0.0514

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.127

Alfa AF: 0.134 Hom.: 126

Bravo AF: 0.125

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524077; hg19: chr6-31243603; COSMIC: COSV66117359; COSMIC: COSV66117359;