rs9721620

Variant names:

• chr9-133514954-A-C
• rs9721620
• NM_001080483.3:c.517-169T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• Carey-Fineman-Ziter syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Illumina, Genomics England PanelApp, Orphanet
• Carey-Fineman-Ziter syndrome 1

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080483.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYMK	NM_001080483.3	MANE Select	c.517-169T>G		intron	N/A	NP_001073952.1	A6NI61

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYMK	ENST00000339996.4	TSL:2 MANE Select	c.517-169T>G		intron	N/A	ENSP00000419712.2	A6NI61

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

African (AFR) AF: 0.217 AC: 9006 AN: 41426

American (AMR) AF: 0.228 AC: 3480 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3466

East Asian (EAS) AF: 0.0329 AC: 170 AN: 5160

South Asian (SAS) AF: 0.0664 AC: 319 AN: 4804

European-Finnish (FIN) AF: 0.230 AC: 2427 AN: 10566

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19678 AN: 67876

Other (OTH) AF: 0.259 AC: 547 AN: 2112

Alfa AF: 0.257 Hom.: 3446

Bravo AF: 0.245

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.73
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9721620; hg19: chr9-136380076;