Variant rs79738065 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_002469.3(MYF6):c.*19C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0254 in 1,562,002 control chromosomes in the GnomAD database, including 634 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 38 hom., cov: 32)

Exomes 𝑓: 0.026 ( 596 hom. )

Consequence

MYF6
NM_002469.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.560

Variant links:

Genes affected

MYF6 (HGNC:7566): (myogenic factor 6) The protein encoded by this gene is a probable basic helix-loop-helix (bHLH) DNA binding protein involved in muscle differentiation. The encoded protein likely acts as a heterodimer with another bHLH protein. Defects in this gene are a cause of autosomal dominant centronuclear myopathy (ADCNM). [provided by RefSeq, May 2010]

MYF6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 12-80708979-C-A is Benign according to our data. Variant chr12-80708979-C-A is described in ClinVar as [Benign]. Clinvar id is 258665.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-80708979-C-A is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0177 (2700/152336) while in subpopulation NFE AF= 0.0287 (1951/68028). AF 95% confidence interval is 0.0276. There are 38 homozygotes in gnomad4. There are 1220 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2700 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYF6	NM_002469.3 linkuse as main transcript	c.*19C>A		3_prime_UTR_variant	3/3	ENST00000228641.4	NP_002460.1	P23409

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYF6	ENST00000228641.4 linkuse as main transcript	c.*19C>A		3_prime_UTR_variant	3/3	1	NM_002469.3	ENSP00000228641.3		P23409

Frequencies

GnomAD3 genomes

AF:

0.0177

AC:

2701

AN:

152218

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00564

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.0115

Gnomad ASJ

AF:

0.00807

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0145

Gnomad FIN

AF:

0.0132

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0287

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.0198

AC:

4960

AN:

251062

Hom.:

AF XY:

0.0201

AC XY:

2732

AN XY:

135726

show subpopulations

Gnomad AFR exome

AF:

0.00604

Gnomad AMR exome

AF:

0.0116

Gnomad ASJ exome

AF:

0.00735

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0181

Gnomad FIN exome

AF:

0.0152

Gnomad NFE exome

AF:

0.0296

Gnomad OTH exome

AF:

0.0233

GnomAD4 exome

AF:

0.0263

AC:

37041

AN:

1409666

Hom.:

596

Cov.:

AF XY:

0.0258

AC XY:

18194

AN XY:

704594

show subpopulations

Gnomad4 AFR exome

AF:

0.00439

Gnomad4 AMR exome

AF:

0.0114

Gnomad4 ASJ exome

AF:

0.00705

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0178

Gnomad4 FIN exome

AF:

0.0172

Gnomad4 NFE exome

AF:

0.0306

Gnomad4 OTH exome

AF:

0.0202

GnomAD4 genome

AF:

0.0177

AC:

2700

AN:

152336

Hom.:

Cov.:

AF XY:

0.0164

AC XY:

1220

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.00563

Gnomad4 AMR

AF:

0.0114

Gnomad4 ASJ

AF:

0.00807

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0143

Gnomad4 FIN

AF:

0.0132

Gnomad4 NFE

AF:

0.0287

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.0219

Hom.:

Bravo

AF:

0.0170

Asia WGS

AF:

0.00808

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

3.9

DANN

Benign

0.76

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