chr17-10445058-T-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_017533.2(MYH4):āc.5384A>Cā(p.Lys1795Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000691 in 1,614,176 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0037 ( 5 hom., cov: 32)
Exomes š: 0.00038 ( 8 hom. )
Consequence
MYH4
NM_017533.2 missense
NM_017533.2 missense
Scores
6
6
6
Clinical Significance
Conservation
PhyloP100: 7.97
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.
BP4
Computational evidence support a benign effect (MetaRNN=0.0154872835).
BP6
Variant 17-10445058-T-G is Benign according to our data. Variant chr17-10445058-T-G is described in ClinVar as [Benign]. Clinvar id is 724790.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 559 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH4 | NM_017533.2 | c.5384A>C | p.Lys1795Thr | missense_variant | 37/40 | ENST00000255381.2 | |
MYHAS | NR_125367.1 | n.167+38820T>G | intron_variant, non_coding_transcript_variant | ||||
MYH4 | XM_017024676.2 | c.5384A>C | p.Lys1795Thr | missense_variant | 35/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH4 | ENST00000255381.2 | c.5384A>C | p.Lys1795Thr | missense_variant | 37/40 | 1 | NM_017533.2 | P1 | |
ENST00000399342.6 | n.206+38781T>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
ENST00000581304.1 | n.143+38820T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00366 AC: 557AN: 152204Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.000871 AC: 219AN: 251478Hom.: 4 AF XY: 0.000670 AC XY: 91AN XY: 135908
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GnomAD4 exome AF: 0.000380 AC: 556AN: 1461854Hom.: 8 Cov.: 42 AF XY: 0.000311 AC XY: 226AN XY: 727230
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GnomAD4 genome AF: 0.00367 AC: 559AN: 152322Hom.: 5 Cov.: 32 AF XY: 0.00330 AC XY: 246AN XY: 74486
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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 | Invitae | Apr 20, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
H
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Pathogenic
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at