rs6503961

chr17-60371741-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032582.4(USP32):c.58+20141T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,102 control chromosomes in the GnomAD database, including 3,209 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 0.14 (3209 hom., cov: 31)
• Consequence: USP32 NM_032582.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

USP32 (HGNC:19143): (ubiquitin specific peptidase 32) Enables thiol-dependent deubiquitinase. Predicted to be involved in protein deubiquitination. Located in Golgi apparatus and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USP32	NM_032582.4	c.58+20141T>C		intron_variant		ENST00000300896.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP32	ENST00000300896.9	c.58+20141T>C		intron_variant		1	NM_032582.4	P1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21197 AN: 151984 Hom.: 3196 Cov.: 31

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0391

Gnomad OTH AF: 0.120

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.140 AC: 21251 AN: 152102 Hom.: 3209 Cov.: 31 AF XY: 0.136 AC XY: 10141 AN XY: 74364

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.0486

Gnomad4 SAS AF: 0.0723

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0390

Gnomad4 OTH AF: 0.119

Alfa AF: 0.111 Hom.: 529

Bravo AF: 0.156

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.3
Dann	Benign	0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6503961; hg19: chr17-58449102;