dbSNP rs1554792556: ZMYND11:p.Arg358Gly (chr10-246887-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_001370100.5(ZMYND11):c.1072C>G(p.Arg358Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R358Q) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

ZMYND11
NM_001370100.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.96

Publications

0 publications found

Variant links:

Genes affected

ZMYND11 (HGNC:16966): (zinc finger MYND-type containing 11) The protein encoded by this gene was first identified by its ability to bind the adenovirus E1A protein. The protein localizes to the nucleus. It functions as a transcriptional repressor, and expression of E1A inhibits this repression. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ZMYND11 Gene-Disease associations (from GenCC):

syndromic complex neurodevelopmental disorder
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
intellectual disability, autosomal dominant 30
Inheritance: AD Classification: STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
autosomal dominant non-syndromic intellectual disability
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ZMYND11 links:

LOC107984190 (HGNC:):

LOC107984190 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;

BP6

Variant 10-246887-C-G is Benign according to our data. Variant chr10-246887-C-G is described in ClinVar as Benign. ClinVar VariationId is 3710679.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370100.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZMYND11	NM_001370100.5	MANE Select	c.1072C>G	p.Arg358Gly	missense	Exon 11 of 15	NP_001357029.1	Q15326-1
ZMYND11	NM_001370097.3		c.1072C>G	p.Arg358Gly	missense	Exon 11 of 15	NP_001357026.1	Q15326-1
ZMYND11	NM_001370098.2		c.1072C>G	p.Arg358Gly	missense	Exon 11 of 15	NP_001357027.1	Q15326-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZMYND11	ENST00000381604.9	TSL:5 MANE Select	c.1072C>G	p.Arg358Gly	missense	Exon 11 of 15	ENSP00000371017.6	Q15326-1
ZMYND11	ENST00000397962.8	TSL:1	c.1072C>G	p.Arg358Gly	missense	Exon 11 of 15	ENSP00000381053.3	Q15326-1
ZMYND11	ENST00000558098.4	TSL:1	c.1072C>G	p.Arg358Gly	missense	Exon 10 of 13	ENSP00000452959.1	Q15326-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.31

BayesDel_addAF

Pathogenic

0.24

BayesDel_noAF

Uncertain

0.11

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.24

Eigen

Uncertain

0.41

Eigen_PC

Uncertain

0.43

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.95

M_CAP

Benign

0.060

MetaRNN

Uncertain

0.45

MetaSVM

Uncertain

-0.25

MutationAssessor

Benign

0.81

PhyloP100

3.0

PrimateAI

Pathogenic

0.84

PROVEAN

Uncertain

-3.6

REVEL

Uncertain

0.43

Sift

Benign

0.033

Sift4G

Benign

0.095

Polyphen

0.95

Vest4

0.62

MVP

0.75

MPC

1.5

ClinPred

0.98

GERP RS

5.4

Varity_R

0.92

gMVP

0.95

Mutation Taster

=35/65

disease causing

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over