Variant chr1-34988170-T-G 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.2912A>C(p.Asn971Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00452 in 1,549,882 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0034 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0047 ( 19 hom. )

Consequence

ZMYM6
NM_007167.4 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.27

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=0.008333147).

BP6

Variant 1-34988170-T-G is Benign according to our data. Variant chr1-34988170-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 3043412.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZMYM6	NM_007167.4 link	c.2912A>C	p.Asn971Thr	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.2912A>C	p.Asn971Thr	missense_variant	16/16	1	NM_007167.4	ENSP00000349708.4	O95789-3
ZMYM6	ENST00000493328.5 link	n.4236A>C		non_coding_transcript_exon_variant	15/15	1
ENSG00000271741	ENST00000487874.1 link	n.2146+4064A>C		intron_variant		5		ENSP00000421752.1

Frequencies

GnomAD3 genomes

AF:

0.00336

AC:

512

AN:

152228

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00452

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00541

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00303

AC:

457

AN:

150846

Hom.:

AF XY:

0.00300

AC XY:

240

AN XY:

80072

show subpopulations

Gnomad AFR exome

AF:

0.000637

Gnomad AMR exome

AF:

0.00339

Gnomad ASJ exome

AF:

0.00366

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000222

Gnomad FIN exome

AF:

0.000590

Gnomad NFE exome

AF:

0.00535

Gnomad OTH exome

AF:

0.00419

GnomAD4 exome

AF:

0.00465

AC:

6500

AN:

1397536

Hom.:

Cov.:

AF XY:

0.00460

AC XY:

3170

AN XY:

689006

show subpopulations

Gnomad4 AFR exome

AF:

0.000730

Gnomad4 AMR exome

AF:

0.00357

Gnomad4 ASJ exome

AF:

0.00278

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000343

Gnomad4 FIN exome

AF:

0.000652

Gnomad4 NFE exome

AF:

0.00554

Gnomad4 OTH exome

AF:

0.00406

GnomAD4 genome

AF:

0.00336

AC:

512

AN:

152346

Hom.:

Cov.:

AF XY:

0.00303

AC XY:

226

AN XY:

74500

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00451

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.00541

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.00506

Hom.:

Bravo

AF:

0.00367

TwinsUK

AF:

0.00485

AC:

ALSPAC

AF:

0.00571

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00570

AC:

ExAC

AF:

0.00237

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ZMYM6-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 05, 2019

This variant is classified as likely 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

0.15

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.011

Eigen

Benign

-0.16

Eigen_PC

Benign

-0.069

FATHMM_MKL

Benign

0.44

LIST_S2

Benign

0.67

M_CAP

Benign

0.0070

MetaRNN

Benign

0.0083

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.5

PrimateAI

Uncertain

0.52

PROVEAN

Benign

-0.86

REVEL

Benign

0.0090

Sift

Uncertain

0.016

Sift4G

Benign

0.30

Polyphen

0.19

Vest4

0.34

MVP

0.067

MPC

0.54

ClinPred

0.018

GERP RS

3.2

Varity_R

0.093

gMVP

0.16

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