6-31275393-G-A

Variant names:

• chr6-31275393-G-A
• rs3132486
• ENST00000755297.1:n.32+4287G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+4287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,952 control chromosomes in the GnomAD database, including 18,637 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 0.49 (18637 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80
• Publications: 32 publications found

Genes affected

ENSG00000298396 (HGNC:):

USP8P1 (HGNC:13987): (USP8 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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
	ENSG00000298396	ENST00000755297.1		n.32+4287G>A		intron	N/A
	USP8P1	ENST00000494673.1	TSL:6	n.-179G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74840 AN: 151834 Hom.: 18623 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.469

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.493 AC: 74891 AN: 151952 Hom.: 18637 Cov.: 31 AF XY: 0.491 AC XY: 36460 AN XY: 74264

African (AFR) AF: 0.446 AC: 18457 AN: 41402

American (AMR) AF: 0.483 AC: 7370 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3472

East Asian (EAS) AF: 0.659 AC: 3408 AN: 5170

South Asian (SAS) AF: 0.442 AC: 2127 AN: 4816

European-Finnish (FIN) AF: 0.508 AC: 5353 AN: 10542

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35440 AN: 67968

Other (OTH) AF: 0.470 AC: 988 AN: 2104

Alfa AF: 0.502 Hom.: 29037

Bravo AF: 0.490

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.25
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs3132486; hg19: chr6-31243170;