Genetic Variant ZMYM6:p.Arg737Thr (chr1-34988872-C-G) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_007167.4(ZMYM6):c.2210G>C(p.Arg737Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00165 in 1,610,374 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0017 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0016 ( 24 hom. )

Consequence

ZMYM6
NM_007167.4 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0140

Variant links:

Genes affected

ZMYM6 (HGNC:13050): (zinc finger MYM-type containing 6) Predicted to enable DNA binding activity. Involved in cytoskeleton organization and regulation of cell morphogenesis. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZMYM6 links:

ENSG00000271741 (HGNC:):

ENSG00000271741 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0036462545).

BP6

Variant 1-34988872-C-G is Benign according to our data. Variant chr1-34988872-C-G is described in ClinVar as [Benign]. Clinvar id is 3043128.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-34988872-C-G is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAdExome4 at 24 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZMYM6	NM_007167.4 link	c.2210G>C	p.Arg737Thr	missense_variant	Exon 16 of 16	ENST00000357182.9	NP_009098.3	O95789-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZMYM6	ENST00000357182.9 link	c.2210G>C	p.Arg737Thr	missense_variant	Exon 16 of 16	1	NM_007167.4	ENSP00000349708.4	O95789-3
ZMYM6	ENST00000493328.5 link	n.3534G>C		non_coding_transcript_exon_variant	Exon 15 of 15	1
ENSG00000271741	ENST00000487874.1 link	n.2146+3362G>C		intron_variant	Intron 15 of 16	5		ENSP00000421752.1

Frequencies

GnomAD3 genomes

AF:

0.00174

AC:

265

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00246

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000393

Gnomad ASJ

AF:

0.0156

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.00932

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000662

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00292

AC:

700

AN:

239496

Hom.:

AF XY:

0.00326

AC XY:

425

AN XY:

130234

show subpopulations

Gnomad AFR exome

AF:

0.00240

Gnomad AMR exome

AF:

0.000767

Gnomad ASJ exome

AF:

0.0174

Gnomad EAS exome

AF:

0.00193

Gnomad SAS exome

AF:

0.0109

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000809

Gnomad OTH exome

AF:

0.00389

GnomAD4 exome

AF:

0.00164

AC:

2394

AN:

1458134

Hom.:

Cov.:

AF XY:

0.00191

AC XY:

1387

AN XY:

725002

show subpopulations

Gnomad4 AFR exome

AF:

0.00315

Gnomad4 AMR exome

AF:

0.000766

Gnomad4 ASJ exome

AF:

0.0178

Gnomad4 EAS exome

AF:

0.00144

Gnomad4 SAS exome

AF:

0.0101

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000593

Gnomad4 OTH exome

AF:

0.00266

GnomAD4 genome

AF:

0.00173

AC:

263

AN:

152240

Hom.:

Cov.:

AF XY:

0.00187

AC XY:

139

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00246

Gnomad4 AMR

AF:

0.000393

Gnomad4 ASJ

AF:

0.0156

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.00891

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000662

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00250

Hom.:

Bravo

AF:

0.00161

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00156

AC:

ESP6500AA

AF:

0.00196

AC:

ESP6500EA

AF:

0.00135

AC:

ExAC

AF:

0.00273

AC:

329

Asia WGS

AF:

0.00694

AC:

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ZMYM6-related disorder

Benign:1

Jun 21, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Benign

0.85

DEOGEN2

Benign

0.011

Eigen

Benign

-0.72

Eigen_PC

Benign

-0.71

FATHMM_MKL

Benign

0.23

LIST_S2

Benign

0.76

MetaRNN

Benign

0.0036

MetaSVM

Benign

-0.92

MutationAssessor

Uncertain

2.4

PrimateAI

Benign

0.42

PROVEAN

Benign

-1.2

REVEL

Benign

0.16

Sift

Uncertain

0.012

Sift4G

Uncertain

0.040

Polyphen

0.32

Vest4

0.59

MVP

0.048

MPC

0.50

ClinPred

0.011

GERP RS

1.6

Varity_R

0.082

gMVP

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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