rs10418774

Variant names:

• chr19-58471017-A-C
• rs10418774
• NM_014347.3:c.525A>C

Your query was ambiguous. Multiple possible variants found:

• chr19-58471017-A-C
• chr19-58471017-A-G
• chr19-58471017-A-T

Variant summary

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

The NM_014347.3(ZNF324):​c.525A>C​(p.Arg175Ser) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 34)
• Consequence: ZNF324 NM_014347.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

ZNF324 (HGNC:14096): (zinc finger protein 324) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within with a positive effect on G1/S transition of mitotic cell cycle and cell population proliferation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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=0.09662816).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF324	NM_014347.3	c.525A>C	p.Arg175Ser	missense_variant	Exon 4 of 4	ENST00000196482.4	NP_055162.1
ZNF324	XM_005258713.5	c.540A>C	p.Arg180Ser	missense_variant	Exon 4 of 4		XP_005258770.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF324	ENST00000196482.4	c.525A>C	p.Arg175Ser	missense_variant	Exon 4 of 4	1	NM_014347.3	ENSP00000196482.3
ZNF324	ENST00000536459.6	c.525A>C	p.Arg175Ser	missense_variant	Exon 4 of 4	2		ENSP00000444812.1
ZNF324	ENST00000593925.1	c.99A>C	p.Arg33Ser	missense_variant	Exon 1 of 2	2		ENSP00000471778.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 111

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.25
DANN	Benign	0.72
DEOGEN2	Benign	0.023	.;T;T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.064	N
LIST_S2	Benign	0.61	T;.;T
M_CAP	Benign	0.0093	T
MetaRNN	Benign	0.097	T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	1.8	.;L;L
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-0.52	.;N;N
REVEL	Benign	0.047
Sift	Benign	0.15	.;T;T
Sift4G	Benign	0.44	T;T;T
Polyphen		0.28	.;B;B
Vest4		0.15
MutPred		0.50		Gain of phosphorylation at R175 (P = 0.0186);Gain of phosphorylation at R175 (P = 0.0186);Gain of phosphorylation at R175 (P = 0.0186);
MVP		0.18
MPC		0.76
ClinPred		0.081	T
GERP RS		-2.6
Varity_R		0.070
gMVP		0.16

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: rs10418774; hg19: chr19-58982384;