rs6503965

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP32	XM_011525371.2	c.106+25292A>G		intron_variant	Intron 1 of 33		XP_011523673.1
USP32	XM_011525372.2	c.106+25292A>G		intron_variant	Intron 1 of 33		XP_011523674.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP32	ENST00000588898.1	c.106+25292A>G		intron_variant	Intron 1 of 3	5		ENSP00000467098.1
CHCT1	ENST00000461535.1	c.-61+4412T>C		intron_variant	Intron 1 of 1	2		ENSP00000468617.1
ENSG00000296206	ENST00000737278.1	n.142+3613T>C		intron_variant	Intron 1 of 1

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 v4.3

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;