rs6503961

Variant names:

• chr17-60371741-A-G
• rs6503961
• NM_032582.4:c.58+20141T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032582.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP32	NM_032582.4	MANE Select	c.58+20141T>C		intron	N/A	NP_115971.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP32	ENST00000300896.9	TSL:1 MANE Select	c.58+20141T>C		intron	N/A	ENSP00000300896.3	Q8NFA0-1
	USP32	ENST00000393003.7	TSL:1	c.58+20141T>C		intron	N/A	ENSP00000376727.2	Q8NFA0-2
	USP32	ENST00000923223.1		c.58+20141T>C		intron	N/A	ENSP00000593282.1

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

African (AFR) AF: 0.373 AC: 15432 AN: 41416

American (AMR) AF: 0.114 AC: 1733 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.0486 AC: 252 AN: 5182

South Asian (SAS) AF: 0.0723 AC: 349 AN: 4824

European-Finnish (FIN) AF: 0.0352 AC: 373 AN: 10608

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0390 AC: 2656 AN: 68018

Other (OTH) AF: 0.119 AC: 251 AN: 2110

Alfa AF: 0.107 Hom.: 817

Bravo AF: 0.156

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.89
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6503961; hg19: chr17-58449102;