17-60404137-G-A

Variant names:

• chr17-60404137-G-A
• rs7218904
• ENST00000588898.1:c.106+18109C>T

Variant summary

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

The ENST00000461535.1(CHCT1):​c.-61+11595G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,112 control chromosomes in the GnomAD database, including 9,046 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 0.22 (9046 hom., cov: 32)
• Consequence: CHCT1 ENST00000461535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000461535.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP32	ENST00000588898.1	TSL:5	c.106+18109C>T		intron	N/A	ENSP00000467098.1	K7ENU6
	CHCT1	ENST00000461535.1	TSL:2	c.-61+11595G>A		intron	N/A	ENSP00000468617.1	A0A0G2JLI9
	ENSG00000296206	ENST00000737278.1		n.143-10735G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33201 AN: 151994 Hom.: 9006 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0472

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.219 AC: 33292 AN: 152112 Hom.: 9046 Cov.: 32 AF XY: 0.213 AC XY: 15841 AN XY: 74360

African (AFR) AF: 0.644 AC: 26708 AN: 41452

American (AMR) AF: 0.148 AC: 2260 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0472 AC: 164 AN: 3472

East Asian (EAS) AF: 0.0482 AC: 250 AN: 5184

South Asian (SAS) AF: 0.0740 AC: 357 AN: 4824

European-Finnish (FIN) AF: 0.0360 AC: 381 AN: 10594

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0404 AC: 2748 AN: 67998

Other (OTH) AF: 0.178 AC: 375 AN: 2110

Alfa AF: 0.102 Hom.: 749

Bravo AF: 0.247

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.63
PhyloP100		-0.38

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7218904;

hg19: chr17-58481498;