9-133514954-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.95

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]

ACMG classification

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	UniProt
MYMK	NM_001080483.3	c.517-169T>G		intron_variant		ENST00000339996.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYMK	ENST00000339996.4	c.517-169T>G		intron_variant		2	NM_001080483.3	P1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36709 AN: 151758 Hom.: 4800 Cov.: 33

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.: 33 AF XY: 0.236 AC XY: 17538 AN XY: 74230

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

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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

Other links and lift over

dbSNP: rs9721620; hg19: chr9-136380076;