rs7381988

Variant names:

• chr6-31278926-G-A
• rs7381988

Your query was ambiguous. Multiple possible variants found:

• chr6-31278926-G-A
• chr6-31278926-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP8P1		n.31278926G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1	n.32+7820G>A		intron_variant	Intron 1 of 1
USP8P1	ENST00000494673.1	n.*172G>A		downstream_gene_variant		6

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 v4.3

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;