rs2524073

Variant names:

• chr6-31276458-G-A
• rs2524073
• ENST00000494673.1:n.887G>A

Variant summary

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

The ENST00000494673.1(USP8P1):​n.887G>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 0.106 in 758,738 control chromosomes in the GnomAD database, including 4,946 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 0.11 (1036 hom., cov: 33)
  • Exomes 𝑓: 0.10 (3910 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 13 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 (NFE) allele frequency at 95% confidence interval = 0.122 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

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
	USP8P1	ENST00000494673.1	TSL:6	n.887G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+5352G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17258 AN: 152106 Hom.: 1035 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.122

GnomAD4 exome AF: 0.104 AC: 63290 AN: 606512 Hom.: 3910 Cov.: 7 AF XY: 0.101 AC XY: 32474 AN XY: 322596

African (AFR) AF: 0.105 AC: 1631 AN: 15588

American (AMR) AF: 0.124 AC: 3112 AN: 25110

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 1987 AN: 14392

East Asian (EAS) AF: 0.0921 AC: 2963 AN: 32168

South Asian (SAS) AF: 0.0421 AC: 2291 AN: 54382

European-Finnish (FIN) AF: 0.0546 AC: 2479 AN: 45424

Middle Eastern (MID) AF: 0.0508 AC: 191 AN: 3762

European-Non Finnish (NFE) AF: 0.117 AC: 45063 AN: 385894

Other (OTH) AF: 0.120 AC: 3573 AN: 29792

GnomAD4 genome AF: 0.113 AC: 17258 AN: 152226 Hom.: 1036 Cov.: 33 AF XY: 0.108 AC XY: 8058 AN XY: 74442

African (AFR) AF: 0.112 AC: 4639 AN: 41514

American (AMR) AF: 0.119 AC: 1817 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3470

East Asian (EAS) AF: 0.103 AC: 534 AN: 5184

South Asian (SAS) AF: 0.0706 AC: 341 AN: 4830

European-Finnish (FIN) AF: 0.0527 AC: 559 AN: 10612

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8465 AN: 68004

Other (OTH) AF: 0.121 AC: 255 AN: 2110

Alfa AF: 0.120 Hom.: 1477

Bravo AF: 0.120

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.9
DANN	Benign	0.84
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs2524073; hg19: chr6-31244235; COSMIC: COSV66117364; COSMIC: COSV66117364;