rs2524074

Variant names:

• chr6-31276244-G-A
• rs2524074
• ENST00000494673.1:n.673G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31276244-G-A
• chr6-31276244-G-C
• chr6-31276244-G-T

Variant summary

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

The ENST00000494673.1(USP8P1):​n.673G>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 0.73 in 742,770 control chromosomes in the GnomAD database, including 200,532 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 0.75 (43214 hom., cov: 31)
  • Exomes 𝑓: 0.72 (157318 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 39 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=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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.673G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+5138G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114167 AN: 152038 Hom.: 43180 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.783

GnomAD4 exome AF: 0.725 AC: 427976 AN: 590614 Hom.: 157318 Cov.: 5 AF XY: 0.727 AC XY: 233607 AN XY: 321336

African (AFR) AF: 0.799 AC: 12758 AN: 15958

American (AMR) AF: 0.760 AC: 27691 AN: 36440

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 14991 AN: 17326

East Asian (EAS) AF: 0.853 AC: 30536 AN: 35778

South Asian (SAS) AF: 0.770 AC: 48031 AN: 62398

European-Finnish (FIN) AF: 0.730 AC: 36258 AN: 49648

Middle Eastern (MID) AF: 0.812 AC: 2949 AN: 3630

European-Non Finnish (NFE) AF: 0.686 AC: 232324 AN: 338600

Other (OTH) AF: 0.728 AC: 22438 AN: 30836

GnomAD4 genome AF: 0.751 AC: 114249 AN: 152156 Hom.: 43214 Cov.: 31 AF XY: 0.755 AC XY: 56190 AN XY: 74402

African (AFR) AF: 0.817 AC: 33892 AN: 41482

American (AMR) AF: 0.779 AC: 11916 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3034 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4277 AN: 5182

South Asian (SAS) AF: 0.774 AC: 3734 AN: 4826

European-Finnish (FIN) AF: 0.737 AC: 7801 AN: 10588

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47072 AN: 67990

Other (OTH) AF: 0.783 AC: 1654 AN: 2112

Alfa AF: 0.714 Hom.: 152805

Bravo AF: 0.755

Asia WGS AF: 0.801 AC: 2786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		-0.073

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2524074;

hg19: chr6-31244021;