rs3130696

Variant names:

• chr6-31276107-G-A
• rs3130696
• ENST00000494673.1:n.536G>A

Variant summary

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

The ENST00000494673.1(USP8P1):​n.536G>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 0.279 in 1,046,220 control chromosomes in the GnomAD database, including 47,284 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 0.24 (4408 hom., cov: 32)
  • Exomes 𝑓: 0.29 (42876 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466
• Publications: 33 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000494673.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP8P1	ENST00000494673.1	TSL:6	n.536G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+5001G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36025 AN: 152014 Hom.: 4396 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.248

GnomAD4 exome AF: 0.286 AC: 255325 AN: 894088 Hom.: 42876 Cov.: 14 AF XY: 0.279 AC XY: 130533 AN XY: 467372

African (AFR) AF: 0.286 AC: 6038 AN: 21102

American (AMR) AF: 0.200 AC: 8747 AN: 43724

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 3382 AN: 21008

East Asian (EAS) AF: 0.297 AC: 11061 AN: 37238

South Asian (SAS) AF: 0.197 AC: 14368 AN: 73018

European-Finnish (FIN) AF: 0.204 AC: 10694 AN: 52500

Middle Eastern (MID) AF: 0.232 AC: 1002 AN: 4324

European-Non Finnish (NFE) AF: 0.315 AC: 189091 AN: 600106

Other (OTH) AF: 0.266 AC: 10942 AN: 41068

GnomAD4 genome AF: 0.237 AC: 36068 AN: 152132 Hom.: 4408 Cov.: 32 AF XY: 0.235 AC XY: 17460 AN XY: 74378

African (AFR) AF: 0.242 AC: 10031 AN: 41490

American (AMR) AF: 0.232 AC: 3549 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1324 AN: 5172

South Asian (SAS) AF: 0.197 AC: 952 AN: 4824

European-Finnish (FIN) AF: 0.197 AC: 2085 AN: 10582

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16831 AN: 67990

Other (OTH) AF: 0.249 AC: 525 AN: 2110

Alfa AF: 0.246 Hom.: 14270

Bravo AF: 0.243

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	15
DANN	Benign	0.31
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs3130696; hg19: chr6-31243884; COSMIC: COSV66119925; COSMIC: COSV66119925;