17-9645788-C-A

Variant names:

• chr17-9645788-C-A
• rs1911342855
• NM_153210.5:c.156C>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_153210.5(USP43):​c.156C>A​(p.His52Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000161 in 1,240,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: USP43 NM_153210.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.196

Genes affected

USP43 (HGNC:20072): (ubiquitin specific peptidase 43) Predicted to enable ISG15-specific protease activity. Predicted to be involved in translesion synthesis. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CFAP52 (HGNC:16053): (cilia and flagella associated protein 52) WD repeat-containing proteins, such as WDR16, play crucial roles in a wide range of physiologic functions, including signal transduction, RNA processing, remodeling the cytoskeleton, regulation of vesicular traffic, and cell division (Silva et al., 2005 [PubMed 15967112]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.048327446).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP43	NM_153210.5	c.156C>A	p.His52Gln	missense_variant	Exon 1 of 15	ENST00000285199.12	NP_694942.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP43	ENST00000285199.12	c.156C>A	p.His52Gln	missense_variant	Exon 1 of 15	1	NM_153210.5	ENSP00000285199.6
USP43	ENST00000570475.5	c.156C>A	p.His52Gln	missense_variant	Exon 1 of 15	1		ENSP00000458963.1
USP43	ENST00000570827.6	n.645+446C>A		intron_variant	Intron 1 of 14	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000161 AC: 2 AN: 1240590 Hom.: 0 Cov.: 30 AF XY: 0.00000330 AC XY: 2 AN XY: 605708

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000555

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.86e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Sep 09, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.156C>A (p.H52Q) alteration is located in exon 1 (coding exon 1) of the USP43 gene. This alteration results from a C to A substitution at nucleotide position 156, causing the histidine (H) at amino acid position 52 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.084
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.71
DEOGEN2	Benign	0.020	.;T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.16	T;T
M_CAP	Benign	0.036	D
MetaRNN	Benign	0.048	T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	0.90	L;L
PrimateAI	Pathogenic	0.83	D
PROVEAN	Benign	-0.56	.;N
REVEL	Benign	0.065
Sift	Benign	0.21	.;T
Sift4G	Benign	0.32	T;T
Polyphen		0.0030	.;B
Vest4		0.044
MutPred		0.21		Loss of catalytic residue at H52 (P = 0.0269);Loss of catalytic residue at H52 (P = 0.0269);
MVP		0.21
MPC		0.50
ClinPred		0.070	T
GERP RS		2.6
Varity_R		0.041
gMVP		0.15

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: rs1911342855; hg19: chr17-9549105;