chr17-10445037-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_017533.2(MYH4):āc.5405A>Gā(p.Asp1802Gly) variant causes a missense change. The variant allele was found at a frequency of 0.379 in 1,613,872 control chromosomes in the GnomAD database, including 124,462 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: š 0.36 ( 11081 hom., cov: 32)
Exomes š: 0.38 ( 113381 hom. )
Consequence
MYH4
NM_017533.2 missense
NM_017533.2 missense
Scores
4
7
7
Clinical Significance
Conservation
PhyloP100: 6.23
Genes affected
MYH4 (HGNC:7574): (myosin heavy chain 4) Enables double-stranded RNA binding activity. Involved in muscle contraction. Located in myofibril. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 17-10445037-T-C is Benign according to our data. Variant chr17-10445037-T-C is described in ClinVar as [Benign]. Clinvar id is 1225242.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH4 | NM_017533.2 | c.5405A>G | p.Asp1802Gly | missense_variant | 37/40 | ENST00000255381.2 | |
MYHAS | NR_125367.1 | n.167+38799T>C | intron_variant, non_coding_transcript_variant | ||||
MYH4 | XM_017024676.2 | c.5405A>G | p.Asp1802Gly | missense_variant | 35/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH4 | ENST00000255381.2 | c.5405A>G | p.Asp1802Gly | missense_variant | 37/40 | 1 | NM_017533.2 | P1 | |
ENST00000399342.6 | n.206+38760T>C | intron_variant, non_coding_transcript_variant | 3 | ||||||
ENST00000581304.1 | n.143+38799T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.364 AC: 55331AN: 151906Hom.: 11082 Cov.: 32
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GnomAD3 exomes AF: 0.437 AC: 109971AN: 251462Hom.: 26905 AF XY: 0.434 AC XY: 59015AN XY: 135900
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GnomAD4 exome AF: 0.381 AC: 556496AN: 1461848Hom.: 113381 Cov.: 103 AF XY: 0.384 AC XY: 278908AN XY: 727228
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GnomAD4 genome AF: 0.364 AC: 55353AN: 152024Hom.: 11081 Cov.: 32 AF XY: 0.376 AC XY: 27947AN XY: 74310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 09, 2020 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
MutationTaster
Benign
P
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MPC
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at