19-34933703-A-T

Position:

• chr19-34933703-A-T

Variant summary

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

The NM_194325.3(ZNF30):​c.236A>T​(p.Asp79Val) 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 Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF30 NM_194325.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.19

Genes affected

ZNF30 (HGNC:13090): (zinc finger protein 30) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF30 (HGNC:):

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=0.07552791).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF30	NM_194325.3	c.236A>T	p.Asp79Val	missense_variant	4/5	ENST00000601142.2	NP_919306.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF30	ENST00000601142.2	c.236A>T	p.Asp79Val	missense_variant	4/5	2	NM_194325.3	ENSP00000469954.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 12, 2023

The c.239A>T (p.D80V) alteration is located in exon 4 (coding exon 3) of the ZNF30 gene. This alteration results from a A to T substitution at nucleotide position 239, causing the aspartic acid (D) at amino acid position 80 to be replaced by a valine (V). 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	0.12
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.7
DANN	Benign	0.22
DEOGEN2	Benign	0.015	.;.;.;.;T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.0077	N
LIST_S2	Benign	0.12	.;T;T;T;T
M_CAP	Benign	0.0022	T
MetaRNN	Benign	0.076	T;T;T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	0.41	.;.;.;N;N
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-1.2	.;N;.;.;.
REVEL	Benign	0.049
Sift	Benign	0.29	.;T;.;.;.
Sift4G	Benign	0.23	T;T;T;T;T
Polyphen		0.0050	B;B;.;.;B
Vest4		0.41
MutPred		0.48		.;.;.;Gain of MoRF binding (P = 0.0202);Gain of MoRF binding (P = 0.0202);
MVP		0.28
MPC		0.038
ClinPred		0.031	T
GERP RS		1.4
Varity_R		0.092
gMVP		0.050

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: rs1568538231; hg19: chr19-35424607;