18-58918955-C-T

Position:

• chr18-58918955-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_001375912.1(ZNF532):​c.668C>T​(p.Ala223Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF532 NM_001375912.1 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0390

Genes affected

ZNF532 (HGNC:30940): (zinc finger protein 532) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.022504896).
• BP6: Variant 18-58918955-C-T is Benign according to our data. Variant chr18-58918955-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3476751.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF532	NM_001375912.1	c.668C>T	p.Ala223Val	missense_variant	3/10	ENST00000591808.6	NP_001362841.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF532	ENST00000591808.6	c.668C>T	p.Ala223Val	missense_variant	3/10	1	NM_001375912.1	ENSP00000468238.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 11, 2024

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.4
DANN	Benign	0.88
DEOGEN2	Benign	0.015	T;T;T;T;T
Eigen	Benign	-0.92
Eigen_PC	Benign	-0.88
FATHMM_MKL	Benign	0.043	N
LIST_S2	Benign	0.78	.;.;.;.;T
M_CAP	Benign	0.0068	T
MetaRNN	Benign	0.023	T;T;T;T;T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	0.20	N;N;N;N;N
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-0.52	N;.;.;.;.
REVEL	Benign	0.061
Sift	Benign	0.14	T;.;.;.;.
Sift4G	Benign	0.45	T;T;T;T;T
Polyphen		0.0	B;B;B;B;B
Vest4		0.019
MutPred		0.19		Gain of methylation at K222 (P = 0.0365);Gain of methylation at K222 (P = 0.0365);Gain of methylation at K222 (P = 0.0365);Gain of methylation at K222 (P = 0.0365);Gain of methylation at K222 (P = 0.0365);
MVP		0.068
MPC		0.54
ClinPred		0.014	T
GERP RS		0.84
Varity_R		0.034
gMVP		0.013

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-56586187;