rs9461680

Variant names:

• chr6-31275570-C-T
• rs9461680
• ENST00000755297.1:n.32+4464C>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+4464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 339,942 control chromosomes in the GnomAD database, including 6,849 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 0.19 (2970 hom., cov: 33)
  • Exomes 𝑓: 0.19 (3879 hom.)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 24 publications found

Genes affected

ENSG00000298396 (HGNC:):

USP8P1 (HGNC:13987): (USP8 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1	n.32+4464C>T		intron_variant	Intron 1 of 1
USP8P1	ENST00000494673.1	n.-2C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29611 AN: 151882 Hom.: 2967 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.187 AC: 35089 AN: 187942 Hom.: 3879 Cov.: 0 AF XY: 0.183 AC XY: 18723 AN XY: 102222

African (AFR) AF: 0.167 AC: 679 AN: 4068

American (AMR) AF: 0.136 AC: 1162 AN: 8560

Ashkenazi Jewish (ASJ) AF: 0.0915 AC: 388 AN: 4240

East Asian (EAS) AF: 0.231 AC: 2501 AN: 10836

South Asian (SAS) AF: 0.198 AC: 5019 AN: 25370

European-Finnish (FIN) AF: 0.254 AC: 4174 AN: 16418

Middle Eastern (MID) AF: 0.175 AC: 123 AN: 704

European-Non Finnish (NFE) AF: 0.179 AC: 19288 AN: 107978

Other (OTH) AF: 0.180 AC: 1755 AN: 9768

GnomAD4 genome AF: 0.195 AC: 29621 AN: 152000 Hom.: 2970 Cov.: 33 AF XY: 0.199 AC XY: 14761 AN XY: 74282

African (AFR) AF: 0.189 AC: 7855 AN: 41458

American (AMR) AF: 0.197 AC: 3009 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0847 AC: 294 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1549 AN: 5174

South Asian (SAS) AF: 0.201 AC: 968 AN: 4826

European-Finnish (FIN) AF: 0.261 AC: 2752 AN: 10528

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12703 AN: 67946

Other (OTH) AF: 0.164 AC: 346 AN: 2116

Alfa AF: 0.192 Hom.: 5723

Bravo AF: 0.189

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.9
DANN	Benign	0.62
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs9461680; hg19: chr6-31243347;