Genetic Variant MYMK:p.Tyr178Tyr (chr9-133514768-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001080483.3(MYMK):c.534T>C(p.Tyr178Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 1,613,678 control chromosomes in the GnomAD database, including 324,082 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.63 ( 30203 hom., cov: 33)

Exomes 𝑓: 0.63 ( 293879 hom. )

Consequence

MYMK
NM_001080483.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0680

Variant links:

Genes affected

MYMK (HGNC:33778): (myomaker, myoblast fusion factor) Involved in myoblast fusion. Located in plasma membrane. Implicated in Carey-Fineman-Ziter syndrome. [provided by Alliance of Genome Resources, Apr 2022]

MYMK links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 9-133514768-A-G is Benign according to our data. Variant chr9-133514768-A-G is described in ClinVar as [Benign]. Clinvar id is 1179965.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYMK	NM_001080483.3 link	c.534T>C	p.Tyr178Tyr	synonymous_variant	Exon 5 of 5	ENST00000339996.4	NP_001073952.1	A6NI61

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYMK	ENST00000339996.4 link	c.534T>C	p.Tyr178Tyr	synonymous_variant	Exon 5 of 5	2	NM_001080483.3	ENSP00000419712.2		A6NI61

Frequencies

GnomAD3 genomes

AF:

0.625

AC:

95029

AN:

152000

Hom.:

30182

Cov.:

show subpopulations

Gnomad AFR

AF:

0.635

Gnomad AMI

AF:

0.669

Gnomad AMR

AF:

0.746

Gnomad ASJ

AF:

0.608

Gnomad EAS

AF:

0.670

Gnomad SAS

AF:

0.536

Gnomad FIN

AF:

0.449

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.621

Gnomad OTH

AF:

0.674

GnomAD3 exomes

AF:

0.620

AC:

155458

AN:

250684

Hom.:

49535

AF XY:

0.611

AC XY:

82739

AN XY:

135450

show subpopulations

Gnomad AFR exome

AF:

0.638

Gnomad AMR exome

AF:

0.781

Gnomad ASJ exome

AF:

0.621

Gnomad EAS exome

AF:

0.664

Gnomad SAS exome

AF:

0.534

Gnomad FIN exome

AF:

0.461

Gnomad NFE exome

AF:

0.614

Gnomad OTH exome

AF:

0.637

GnomAD4 exome

AF:

0.631

AC:

921861

AN:

1461560

Hom.:

293879

Cov.:

AF XY:

0.626

AC XY:

455352

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.634

Gnomad4 AMR exome

AF:

0.779

Gnomad4 ASJ exome

AF:

0.622

Gnomad4 EAS exome

AF:

0.652

Gnomad4 SAS exome

AF:

0.536

Gnomad4 FIN exome

AF:

0.462

Gnomad4 NFE exome

AF:

0.639

Gnomad4 OTH exome

AF:

0.634

GnomAD4 genome

AF:

0.625

AC:

95097

AN:

152118

Hom.:

30203

Cov.:

AF XY:

0.621

AC XY:

46169

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.635

Gnomad4 AMR

AF:

0.746

Gnomad4 ASJ

AF:

0.608

Gnomad4 EAS

AF:

0.670

Gnomad4 SAS

AF:

0.537

Gnomad4 FIN

AF:

0.449

Gnomad4 NFE

AF:

0.621

Gnomad4 OTH

AF:

0.671

Alfa

AF:

0.623

Hom.:

22304

Bravo

AF:

0.653

Asia WGS

AF:

0.628

AC:

2184

AN:

3478

EpiCase

AF:

0.636

EpiControl

AF:

0.642

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 05, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Congenital nonprogressive myopathy with Moebius and Robin sequences

Benign:1

Sep 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

3.9

DANN

Benign

0.75

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