rs3132485

Variant names:

• chr6-31275612-C-A
• rs3132485
• ENST00000494673.1:n.41C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31275612-C-A
• chr6-31275612-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP8P1	ENST00000494673.1	TSL:6	n.41C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+4506C>A		intron	N/A

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

African (AFR) AF: 0.401 AC: 3277 AN: 8174

American (AMR) AF: 0.331 AC: 4652 AN: 14062

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 2661 AN: 7488

East Asian (EAS) AF: 0.362 AC: 6981 AN: 19262

South Asian (SAS) AF: 0.352 AC: 13789 AN: 39158

European-Finnish (FIN) AF: 0.432 AC: 11885 AN: 27526

Middle Eastern (MID) AF: 0.356 AC: 417 AN: 1170

European-Non Finnish (NFE) AF: 0.455 AC: 78787 AN: 172998

Other (OTH) AF: 0.438 AC: 6982 AN: 15934

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

African (AFR) AF: 0.419 AC: 17341 AN: 41426

American (AMR) AF: 0.416 AC: 6353 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2185 AN: 5162

South Asian (SAS) AF: 0.385 AC: 1854 AN: 4812

European-Finnish (FIN) AF: 0.429 AC: 4535 AN: 10560

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32134 AN: 67930

Other (OTH) AF: 0.410 AC: 865 AN: 2108

Alfa AF: 0.447 Hom.: 4716

Bravo AF: 0.441

Asia WGS AF: 0.478 AC: 1662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	9.0
DANN	Benign	0.65
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs3132485; hg19: chr6-31243389;