19-37635495-G-C

Position:

• chr19-37635495-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001320669.3(ZFP30):​c.1046C>G​(p.Thr349Ser) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZFP30 NM_001320669.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.52

Genes affected

ZFP30 (HGNC:29555): (ZFP30 zinc finger protein) 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.29945806).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFP30	NM_001320669.3	c.1046C>G	p.Thr349Ser	missense_variant	6/6	ENST00000684514.1	NP_001307598.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFP30	ENST00000684514.1	c.1046C>G	p.Thr349Ser	missense_variant	6/6		NM_001320669.3	ENSP00000508019.1
ZFP30	ENST00000351218.6	c.1046C>G	p.Thr349Ser	missense_variant	6/6	1		ENSP00000343581.1
ZFP30	ENST00000514101.6	c.1046C>G	p.Thr349Ser	missense_variant	6/6	1		ENSP00000422930.2
ZFP30	ENST00000589018.5	c.232+7770C>G		intron_variant		5		ENSP00000467387.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

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

Mar 04, 2024

The c.1046C>G (p.T349S) alteration is located in exon 6 (coding exon 4) of the ZFP30 gene. This alteration results from a C to G substitution at nucleotide position 1046, causing the threonine (T) at amino acid position 349 to be replaced by a serine (S). 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	0.20
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.18	T;T
Eigen	Uncertain	0.42
Eigen_PC	Uncertain	0.40
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Benign	0.037	.;T
M_CAP	Benign	0.0056	T
MetaRNN	Benign	0.30	T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.52	N;N
PrimateAI	Pathogenic	0.81	D
PROVEAN	Uncertain	-3.1	D;D
REVEL	Benign	0.12
Sift	Benign	0.090	T;T
Sift4G	Benign	0.10	T;T
Polyphen		0.97	D;D
Vest4		0.28
MutPred		0.42		Loss of phosphorylation at T349 (P = 0.0892);Loss of phosphorylation at T349 (P = 0.0892);
MVP		0.45
MPC		0.45
ClinPred		0.96	D
GERP RS		4.0
Varity_R		0.18
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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-38126396;