17-10411058-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002472.3(MYH8):c.1417-111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,553,184 control chromosomes in the GnomAD database, including 128,488 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.38 ( 12118 hom., cov: 32)
Exomes 𝑓: 0.39 ( 116370 hom. )
Consequence
MYH8
NM_002472.3 intron
NM_002472.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.26
Publications
4 publications found
Genes affected
MYH8 (HGNC:7578): (myosin heavy chain 8) Myosins are actin-based motor proteins that function in the generation of mechanical force in eukaryotic cells. Muscle myosins are heterohexamers composed of 2 myosin heavy chains and 2 pairs of nonidentical myosin light chains. This gene encodes a member of the class II or conventional myosin heavy chains, and functions in skeletal muscle contraction. This gene is predominantly expressed in fetal skeletal muscle. This gene is found in a cluster of myosin heavy chain genes on chromosome 17. A mutation in this gene results in trismus-pseudocamptodactyly syndrome. [provided by RefSeq, Sep 2009]
MYHAS (HGNC:50609): (myosin heavy chain gene cluster antisense RNA) Predicted to enable primary miRNA binding activity. Predicted to be involved in response to muscle activity and skeletal muscle fiber development. Predicted to act upstream of or within with a positive effect on gene expression. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
Variant 17-10411058-G-A is Benign according to our data. Variant chr17-10411058-G-A is described in ClinVar as [Benign]. Clinvar id is 1181307.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.379 AC: 57577AN: 151830Hom.: 12109 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
57577
AN:
151830
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.392 AC: 549394AN: 1401236Hom.: 116370 AF XY: 0.398 AC XY: 277141AN XY: 696248 show subpopulations
GnomAD4 exome
AF:
AC:
549394
AN:
1401236
Hom.:
AF XY:
AC XY:
277141
AN XY:
696248
show subpopulations
African (AFR)
AF:
AC:
8444
AN:
31406
American (AMR)
AF:
AC:
22855
AN:
40586
Ashkenazi Jewish (ASJ)
AF:
AC:
10268
AN:
25472
East Asian (EAS)
AF:
AC:
31638
AN:
37350
South Asian (SAS)
AF:
AC:
50414
AN:
82380
European-Finnish (FIN)
AF:
AC:
20585
AN:
48592
Middle Eastern (MID)
AF:
AC:
2172
AN:
5250
European-Non Finnish (NFE)
AF:
AC:
379302
AN:
1072070
Other (OTH)
AF:
AC:
23716
AN:
58130
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
16255
32511
48766
65022
81277
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
12392
24784
37176
49568
61960
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.379 AC: 57623AN: 151948Hom.: 12118 Cov.: 32 AF XY: 0.393 AC XY: 29184AN XY: 74246 show subpopulations
GnomAD4 genome
AF:
AC:
57623
AN:
151948
Hom.:
Cov.:
32
AF XY:
AC XY:
29184
AN XY:
74246
show subpopulations
African (AFR)
AF:
AC:
11441
AN:
41454
American (AMR)
AF:
AC:
7015
AN:
15250
Ashkenazi Jewish (ASJ)
AF:
AC:
1377
AN:
3466
East Asian (EAS)
AF:
AC:
4476
AN:
5168
South Asian (SAS)
AF:
AC:
3052
AN:
4816
European-Finnish (FIN)
AF:
AC:
4599
AN:
10544
Middle Eastern (MID)
AF:
AC:
120
AN:
292
European-Non Finnish (NFE)
AF:
AC:
24389
AN:
67936
Other (OTH)
AF:
AC:
779
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1718
3436
5154
6872
8590
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
572
1144
1716
2288
2860
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2472
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Nov 12, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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