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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP8P1		n.31276244G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP8P1	ENST00000494673.1	n.673G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298396	ENST00000755297.1	n.32+5138G>A		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs2524074; hg19: chr6-31244021;