X-153346878-G-A

Position:

• chrX-153346878-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001367757.1(ZNF275):​c.193G>A​(p.Ala65Thr) 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. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 24)
• Consequence: ZNF275 NM_001367757.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

ZNF275 (HGNC:13069): (zinc finger protein 275) This gene encodes a zinc finger protein that appears to be conserved in eutheria. Its function has not yet been established. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11549044).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF275	NM_001367757.1	c.193G>A	p.Ala65Thr	missense_variant	4/4	ENST00000650114.2
ZNF275	NM_001080485.4	c.193G>A	p.Ala65Thr	missense_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF275	ENST00000650114.2	c.193G>A	p.Ala65Thr	missense_variant	4/4		NM_001367757.1	A2
ZNF275	ENST00000370249.3	c.34G>A	p.Ala12Thr	missense_variant	3/3	1		P2
ZNF275	ENST00000370251.3	c.193G>A	p.Ala65Thr	missense_variant	4/5	2
ZNF275	ENST00000647705.1	n.1405G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Uncertain	0.99
FATHMM_MKL	Benign	0.24	N
LIST_S2	Benign	0.70	T;T;T
M_CAP	Uncertain	0.097	D
MetaRNN	Benign	0.12	T;T;T
MetaSVM	Benign	-1.1	T
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Benign	0.34	T
PROVEAN	Benign	-0.71	N;.;N
REVEL	Benign	0.044
Sift	Benign	0.039	D;.;T
Sift4G	Benign	0.39	T;.;T
Polyphen		0.61, 0.96	.;P;D
Vest4		0.12
MutPred		0.34		.;Gain of relative solvent accessibility (P = 0.0082);Gain of relative solvent accessibility (P = 0.0082);
MVP		0.60
MPC		0.35
ClinPred		0.32	T
GERP RS		3.5
Varity_R		0.069
gMVP		0.037

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: chrX-152612336;