rs2524070

Variant names:

• chr6-31276743-G-A
• rs2524070
• ENST00000494673.1:n.1172G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31276743-G-A
• chr6-31276743-G-C
• chr6-31276743-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.1172G>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 0.179 in 1,156,422 control chromosomes in the GnomAD database, including 19,611 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 0.17 (2253 hom., cov: 32)
  • Exomes 𝑓: 0.18 (17358 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.60
• Publications: 22 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=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP8P1		n.31276743G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP8P1	ENST00000494673.1	n.1172G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298396	ENST00000755297.1	n.32+5637G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25767 AN: 151980 Hom.: 2249 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.178

GnomAD4 exome AF: 0.181 AC: 181323 AN: 1004324 Hom.: 17358 Cov.: 14 AF XY: 0.178 AC XY: 88804 AN XY: 499942

African (AFR) AF: 0.196 AC: 4055 AN: 20728

American (AMR) AF: 0.183 AC: 3905 AN: 21394

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 3032 AN: 15988

East Asian (EAS) AF: 0.108 AC: 3418 AN: 31624

South Asian (SAS) AF: 0.0792 AC: 3767 AN: 47562

European-Finnish (FIN) AF: 0.115 AC: 4875 AN: 42574

Middle Eastern (MID) AF: 0.0973 AC: 363 AN: 3730

European-Non Finnish (NFE) AF: 0.193 AC: 149896 AN: 778638

Other (OTH) AF: 0.190 AC: 8012 AN: 42086

GnomAD4 genome AF: 0.170 AC: 25788 AN: 152098 Hom.: 2253 Cov.: 32 AF XY: 0.164 AC XY: 12220 AN XY: 74382

African (AFR) AF: 0.198 AC: 8204 AN: 41460

American (AMR) AF: 0.155 AC: 2374 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.121 AC: 626 AN: 5182

South Asian (SAS) AF: 0.100 AC: 482 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1151 AN: 10594

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11790 AN: 67986

Other (OTH) AF: 0.178 AC: 375 AN: 2106

Alfa AF: 0.169 Hom.: 8316

Bravo AF: 0.177

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	13
DANN	Benign	0.66
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs2524070; hg19: chr6-31244520;