rs79738065

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 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_single_submitter, 1 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 UniProt
MYF6NM_002469.3 linkuse as main transcriptc.*19C>A 3_prime_UTR_variant 3/3 ENST00000228641.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYF6ENST00000228641.4 linkuse as main transcriptc.*19C>A 3_prime_UTR_variant 3/31 NM_002469.3 P1

Frequencies

GnomAD3 genomes
AF:
0.0177
AC:
2701
AN:
152218
Hom.:
38
Cov.:
32
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.:
89
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.:
26
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.:
38
Cov.:
32
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.:
16
Bravo
AF:
0.0170
Asia WGS
AF:
0.00808
AC:
28
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -

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.

Other links and lift over

dbSNP: rs79738065; hg19: chr12-81102758; API