Variant 1-34988050-A-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_007167.4(ZMYM6):c.3032T>G(p.Phe1011Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00659 in 1,551,608 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0039 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0069 ( 49 hom. )

Consequence

ZMYM6
NM_007167.4 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.23

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.011003286).

BP6

Variant 1-34988050-A-C is Benign according to our data. Variant chr1-34988050-A-C is described in ClinVar as [Benign]. Clinvar id is 3035215.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-34988050-A-C is described in Lovd as [Benign].

BS2

High Homozygotes in GnomAdExome4 at 49 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZMYM6	NM_007167.4 link	c.3032T>G	p.Phe1011Cys	missense_variant	16/16	ENST00000357182.9	NP_009098.3	O95789-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZMYM6	ENST00000357182.9 link	c.3032T>G	p.Phe1011Cys	missense_variant	16/16	1	NM_007167.4	ENSP00000349708.4	O95789-3
ZMYM6	ENST00000493328.5 link	n.4356T>G		non_coding_transcript_exon_variant	15/15	1
ENSG00000271741	ENST00000487874.1 link	n.2147-4103T>G		intron_variant		5		ENSP00000421752.1

Frequencies

GnomAD3 genomes

AF:

0.00387

AC:

589

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00169

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00281

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00669

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00341

AC:

517

AN:

151628

Hom.:

AF XY:

0.00339

AC XY:

273

AN XY:

80504

show subpopulations

Gnomad AFR exome

AF:

0.000890

Gnomad AMR exome

AF:

0.00300

Gnomad ASJ exome

AF:

0.000118

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00144

Gnomad NFE exome

AF:

0.00678

Gnomad OTH exome

AF:

0.00556

GnomAD4 exome

AF:

0.00688

AC:

9633

AN:

1399244

Hom.:

Cov.:

AF XY:

0.00680

AC XY:

4690

AN XY:

690116

show subpopulations

Gnomad4 AFR exome

AF:

0.000981

Gnomad4 AMR exome

AF:

0.00375

Gnomad4 ASJ exome

AF:

0.0000794

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000757

Gnomad4 FIN exome

AF:

0.00140

Gnomad4 NFE exome

AF:

0.00840

Gnomad4 OTH exome

AF:

0.00564

GnomAD4 genome

AF:

0.00387

AC:

589

AN:

152364

Hom.:

Cov.:

AF XY:

0.00337

AC XY:

251

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00168

Gnomad4 AMR

AF:

0.00281

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00113

Gnomad4 NFE

AF:

0.00669

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00598

Hom.:

Bravo

AF:

0.00442

TwinsUK

AF:

0.0105

AC:

ALSPAC

AF:

0.0106

AC:

ExAC

AF:

0.00184

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ZMYM6-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 20, 2019

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

0.20

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.31

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.21

Eigen

Uncertain

0.42

Eigen_PC

Uncertain

0.45

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.69

M_CAP

Benign

0.0091

MetaRNN

Benign

0.011

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.8

PrimateAI

Uncertain

0.49

PROVEAN

Uncertain

-2.4

REVEL

Benign

0.19

Sift

Pathogenic

0.0

Sift4G

Uncertain

0.0040

Polyphen

0.98

Vest4

0.61

MVP

0.27

MPC

0.79

ClinPred

0.044

GERP RS

4.7

Varity_R

0.23

gMVP

0.55

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

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