Variant 19-53576856-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001079906.2(ZNF331):c.296A>T(p.Tyr99Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,886 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

ZNF331
NM_001079906.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.352

Variant links:

Genes affected

ZNF331 (HGNC:15489): (zinc finger protein 331) This gene encodes a zinc finger protein containing a KRAB (Kruppel-associated box) domain found in transcriptional repressors. This gene may be methylated and silenced in cancer cells. This gene is located within a differentially methylated region (DMR) and shows allele-specific expression in placenta. Alternative splicing and the use of alternative promoters results in multiple transcript variants encoding the same protein. [provided by RefSeq, Nov 2015]

ZNF331 links:

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ACMG classification

Classification made for transcript

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=0.12172809).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF331	NM_001079906.2 linkuse as main transcript	c.296A>T	p.Tyr99Phe	missense_variant	6/6	ENST00000449416.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF331	ENST00000449416.6 linkuse as main transcript	c.296A>T	p.Tyr99Phe	missense_variant	6/6	5	NM_001079906.2	P1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000398

AC:

AN:

251456

Hom.:

AF XY:

0.00000736

AC XY:

AN XY:

135902

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000879

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000205

AC:

AN:

1461886

Hom.:

Cov.:

AF XY:

0.00000413

AC XY:

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000270

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 15, 2021

The c.296A>T (p.Y99F) alteration is located in exon 7 (coding exon 3) of the ZNF331 gene. This alteration results from a A to T substitution at nucleotide position 296, causing the tyrosine (Y) at amino acid position 99 to be replaced by a phenylalanine (F). 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

0.10

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.64

CADD

Benign

4.4

DANN

Benign

0.65

DEOGEN2

Benign

0.091

T;T;T;T;T;.;T;T;T;T;T;.;T;T;T;T;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.058

LIST_S2

Benign

0.29

.;.;.;.;T;T;.;.;.;.;.;T;.;T;.;.;.

M_CAP

Benign

0.0033

MetaRNN

Benign

0.067

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

1.3

L;L;L;L;L;.;L;L;L;L;L;.;.;.;L;L;L

MutationTaster

Benign

1.0

D;N;N;N;N;N;N;N

PrimateAI

Benign

0.27

PROVEAN

Benign

-1.7

.;N;.;N;N;N;N;N;.;N;N;N;N;N;.;.;.

REVEL

Benign

0.027

Sift

Benign

0.44

.;T;.;T;T;T;T;T;.;T;T;T;T;T;.;.;.

Sift4G

Benign

0.62

.;T;.;T;T;D;T;T;.;T;T;T;T;T;.;.;.

Polyphen

0.072

B;B;B;B;B;.;B;B;B;B;B;.;.;.;B;B;B

Vest4

0.13, 0.13, 0.12, 0.13, 0.12, 0.14, 0.12

MutPred

0.34

Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);Loss of phosphorylation at Y99 (P = 0.0457);

MVP

0.23

MPC

0.56

ClinPred

0.021

GERP RS

-0.26

Varity_R

0.052

gMVP

0.074

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over