6-31278926-G-A

Variant names:

• chr6-31278926-G-A
• rs7381988

Variant summary

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

The variant allele was found at a frequency of 0.867 in 152,222 control chromosomes in the GnomAD database, including 57,433 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 0.87 (57433 hom., cov: 33)
• Consequence: USP8P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 24 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 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+7820G>A		intron	N/A
	USP8P1	ENST00000494673.1	TSL:6	n.*172G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131944 AN: 152106 Hom.: 57381 Cov.: 33

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.867 AC: 132051 AN: 152222 Hom.: 57433 Cov.: 33 AF XY: 0.868 AC XY: 64577 AN XY: 74422

African (AFR) AF: 0.925 AC: 38442 AN: 41546

American (AMR) AF: 0.868 AC: 13286 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3350 AN: 3472

East Asian (EAS) AF: 0.821 AC: 4255 AN: 5180

South Asian (SAS) AF: 0.863 AC: 4160 AN: 4820

European-Finnish (FIN) AF: 0.830 AC: 8787 AN: 10582

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56833 AN: 68000

Other (OTH) AF: 0.902 AC: 1905 AN: 2112

Alfa AF: 0.854 Hom.: 107470

Bravo AF: 0.874

Asia WGS AF: 0.845 AC: 2940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs7381988; hg19: chr6-31246703;