Variant chr9-133514993-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001080483.3(MYMK):c.517-208T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 150,848 control chromosomes in the GnomAD database, including 10,338 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.36 ( 10338 hom., cov: 32)

Consequence

MYMK
NM_001080483.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.29

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 9-133514993-A-C is Benign according to our data. Variant chr9-133514993-A-C is described in ClinVar as [Benign]. Clinvar id is 1225528.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYMK	NM_001080483.3 linkuse as main transcript	c.517-208T>G		intron_variant		ENST00000339996.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYMK	ENST00000339996.4 linkuse as main transcript	c.517-208T>G		intron_variant		2	NM_001080483.3	P1

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

53814

AN:

150730

Hom.:

10329

Cov.:

show subpopulations

Gnomad AFR

AF:

0.298

Gnomad AMI

AF:

0.290

Gnomad AMR

AF:

0.509

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.635

Gnomad SAS

AF:

0.467

Gnomad FIN

AF:

0.220

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.392

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.357

AC:

53851

AN:

150848

Hom.:

10338

Cov.:

AF XY:

0.359

AC XY:

26409

AN XY:

73612

show subpopulations

Gnomad4 AFR

AF:

0.299

Gnomad4 AMR

AF:

0.509

Gnomad4 ASJ

AF:

0.456

Gnomad4 EAS

AF:

0.635

Gnomad4 SAS

AF:

0.468

Gnomad4 FIN

AF:

0.220

Gnomad4 NFE

AF:

0.345

Gnomad4 OTH

AF:

0.390

Alfa

AF:

0.326

Hom.:

1044

Bravo

AF:

0.376

Asia WGS

AF:

0.507

AC:

1759

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.66

DANN

Benign

0.77

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