Genetic Variant ZMYND15:p.Gly194Arg (chr17-4741128-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001136046.3(ZMYND15):c.580G>A(p.Gly194Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000756 in 1,322,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 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: 7.6e-7 ( 0 hom. )

Consequence

ZMYND15
NM_001136046.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.65

Variant links:

Genes affected

ZMYND15 (HGNC:20997): (zinc finger MYND-type containing 15) This gene encodes a MYND-containing zinc-binding protein with a nuclear localization sequence. A similar gene in mice has been shown to act as a testis-specific transcriptional repressor by recruiting histone deacetylase enzymes to regulate spatiotemporal expression of many haploid genes. This protein may play an important role in spermatogenesis. Alternative splicing results in multiple transcript variants and protein isoforms. [provided by RefSeq, Jun 2012]

ZMYND15 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.19991466).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZMYND15	NM_001136046.3 link	c.580G>A	p.Gly194Arg	missense_variant	Exon 2 of 14	ENST00000433935.6	NP_001129518.1	Q9H091-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZMYND15	ENST00000433935.6 link	c.580G>A	p.Gly194Arg	missense_variant	Exon 2 of 14	2	NM_001136046.3	ENSP00000391742.1		Q9H091-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

98616

AF XY:

0.00

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 FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

7.56e-7

AC:

AN:

1322864

Hom.:

Cov.:

AF XY:

0.00000155

AC XY:

AN XY:

643348

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

29388

American (AMR)

AF:

0.00

AC:

AN:

25446

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20348

East Asian (EAS)

AF:

0.00

AC:

AN:

34712

South Asian (SAS)

AF:

0.00

AC:

AN:

67588

European-Finnish (FIN)

AF:

0.00

AC:

AN:

47044

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5074

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1038624

Other (OTH)

AF:

0.0000183

AC:

AN:

54640

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000510

Hom.:

Bravo

AF:

0.00000378

ExAC

AF:

0.0000105

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

May 02, 2024

Ambry Genetics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The c.580G>A (p.G194R) alteration is located in exon 2 (coding exon 1) of the ZMYND15 gene. This alteration results from a G to A substitution at nucleotide position 580, causing the glycine (G) at amino acid position 194 to be replaced by an arginine (R). 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

0.14

BayesDel_addAF

Benign

-0.051

BayesDel_noAF

Benign

-0.31

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.077

.;T;.;.

Eigen

Uncertain

0.45

Eigen_PC

Uncertain

0.44

FATHMM_MKL

Uncertain

0.94

LIST_S2

Uncertain

0.86

D;D;D;.

M_CAP

Benign

0.030

MetaRNN

Benign

0.20

T;T;T;T

MetaSVM

Benign

-0.66

MutationAssessor

Benign

1.0

L;L;L;L

PhyloP100

4.6

PrimateAI

Benign

0.38

PROVEAN

Benign

-1.3

N;N;.;.

REVEL

Benign

0.20

Sift

Uncertain

0.0020

D;D;.;.

Sift4G

Uncertain

0.0070

D;D;D;D

Polyphen

1.0

.;D;.;.

Vest4

0.31

MutPred

0.20

Loss of ubiquitination at K193 (P = 0.0284);Loss of ubiquitination at K193 (P = 0.0284);Loss of ubiquitination at K193 (P = 0.0284);Loss of ubiquitination at K193 (P = 0.0284);

MVP

0.73

MPC

0.75

ClinPred

0.81

GERP RS

5.3

Varity_R

0.25

gMVP

0.38

Mutation Taster

=95/5

polymorphism

(source)

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 for variant 17:4741128 G>A . It may be empty.

chr17-4741128-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over