6-31279290-T-G

Variant names:

• chr6-31279290-T-G
• rs7382297

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 0.881 in 152,182 control chromosomes in the GnomAD database, including 59,228 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 0.88 (59228 hom., cov: 32)
• Consequence: USP8P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 47 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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298396	ENST00000755297.1		n.32+8184T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.881 AC: 134003 AN: 152066 Hom.: 59173 Cov.: 32

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.881 AC: 134113 AN: 152182 Hom.: 59228 Cov.: 32 AF XY: 0.882 AC XY: 65580 AN XY: 74386

African (AFR) AF: 0.933 AC: 38764 AN: 41528

American (AMR) AF: 0.880 AC: 13452 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3374 AN: 3470

East Asian (EAS) AF: 0.835 AC: 4318 AN: 5174

South Asian (SAS) AF: 0.873 AC: 4212 AN: 4826

European-Finnish (FIN) AF: 0.851 AC: 9003 AN: 10580

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58016 AN: 67996

Other (OTH) AF: 0.908 AC: 1917 AN: 2112

Alfa AF: 0.868 Hom.: 203405

Bravo AF: 0.886

Asia WGS AF: 0.878 AC: 3052 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	19
DANN	Benign	0.72
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs7382297; hg19: chr6-31247067;