ENST00000588898.1:c.106+25292A>G

Variant names:

• chr17-60396954-T-C
• rs6503965
• ENST00000588898.1:c.106+25292A>G

Variant summary

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

The ENST00000588898.1(USP32):​c.106+25292A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,152 control chromosomes in the GnomAD database, including 12,856 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 0.31 (12856 hom., cov: 32)
• Consequence: USP32 ENST00000588898.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 4 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]

CHCT1 (HGNC:26990): (CHD1 helical C-terminal domain containing 1)

ENSG00000296206 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000588898.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP32	ENST00000588898.1	TSL:5	c.106+25292A>G		intron	N/A	ENSP00000467098.1
	CHCT1	ENST00000461535.1	TSL:2	c.-61+4412T>C		intron	N/A	ENSP00000468617.1
	ENSG00000296206	ENST00000737278.1		n.142+3613T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46297 AN: 152034 Hom.: 12795 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.305 AC: 46416 AN: 152152 Hom.: 12856 Cov.: 32 AF XY: 0.297 AC XY: 22126 AN XY: 74402

African (AFR) AF: 0.744 AC: 30853 AN: 41476

American (AMR) AF: 0.195 AC: 2989 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3466

East Asian (EAS) AF: 0.212 AC: 1098 AN: 5168

South Asian (SAS) AF: 0.153 AC: 740 AN: 4826

European-Finnish (FIN) AF: 0.109 AC: 1159 AN: 10590

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.125 AC: 8475 AN: 68020

Other (OTH) AF: 0.257 AC: 542 AN: 2112

Alfa AF: 0.187 Hom.: 6979

Bravo AF: 0.333

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.38
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs6503965; hg19: chr17-58474315;