Variant 9-133514954-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.517-169T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,876 control chromosomes in the GnomAD database, including 4,796 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4796 hom., cov: 33)

Consequence

MYMK
NM_001080483.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.95

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 9-133514954-A-C is Benign according to our data. Variant chr9-133514954-A-C is described in ClinVar as [Benign]. Clinvar id is 1286504.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYMK	NM_001080483.3 link	c.517-169T>G		intron_variant		ENST00000339996.4	NP_001073952.1	A6NI61

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYMK	ENST00000339996.4 link	c.517-169T>G		intron_variant		2	NM_001080483.3	ENSP00000419712.2		A6NI61

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36709

AN:

151758

Hom.:

4800

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.393

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.0329

Gnomad SAS

AF:

0.0668

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.290

Gnomad OTH

AF:

0.263

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

GnomAD4 genome

AF:

0.242

AC:

36721

AN:

151876

Hom.:

4796

Cov.:

AF XY:

0.236

AC XY:

17538

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.228

Gnomad4 ASJ

AF:

0.196

Gnomad4 EAS

AF:

0.0329

Gnomad4 SAS

AF:

0.0664

Gnomad4 FIN

AF:

0.230

Gnomad4 NFE

AF:

0.290

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.260

Hom.:

709

Bravo

AF:

0.245

Asia WGS

AF:

0.0840

AC:

293

AN:

3478

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

-0.95

CADD

Benign

1.0

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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