rs787634

chr10-93360162-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013451.4(MYOF):c.2975-184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,194 control chromosomes in the GnomAD database, including 7,923 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7923 hom., cov: 33)
• Consequence: MYOF NM_013451.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

MYOF (HGNC:3656): (myoferlin) Mutations in dysferlin, a protein associated with the plasma membrane, can cause muscle weakness that affects both proximal and distal muscles. The protein encoded by this gene is a type II membrane protein that is structurally similar to dysferlin. It is a member of the ferlin family and associates with both plasma and nuclear membranes. The protein contains C2 domains that play a role in calcium-mediated membrane fusion events, suggesting that it may be involved in membrane regeneration and repair. Two transcript variants encoding different isoforms have been found for this gene. Other possible variants have been detected, but their full-length nature has not been determined. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYOF	NM_013451.4	c.2975-184A>G		intron_variant		ENST00000359263.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYOF	ENST00000359263.9	c.2975-184A>G		intron_variant		1	NM_013451.4	P1
MYOF	ENST00000358334.9	c.2936-184A>G		intron_variant		1
MYOF	ENST00000463743.5	c.1099-184A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45816 AN: 152076 Hom.: 7920 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.0961

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.301 AC: 45835 AN: 152194 Hom.: 7923 Cov.: 33 AF XY: 0.297 AC XY: 22125 AN XY: 74410

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.0963

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.306

Alfa AF: 0.315 Hom.: 1189

Bravo AF: 0.280

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.5
Dann	Benign	0.40

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

Other links and lift over

dbSNP: rs787634; hg19: chr10-95119919;