rs61730806
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_002472.3(MYH8):āc.4740A>Cā(p.Ala1580=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000571 in 1,614,186 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0032 ( 2 hom., cov: 32)
Exomes š: 0.00030 ( 3 hom. )
Consequence
MYH8
NM_002472.3 synonymous
NM_002472.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.65
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 17-10395355-T-G is Benign according to our data. Variant chr17-10395355-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 211565.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-3.65 with no splicing effect.
BS2
?
High AC in GnomAd4 at 482 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH8 | NM_002472.3 | c.4740A>C | p.Ala1580= | synonymous_variant | 34/40 | ENST00000403437.2 | |
MYHAS | NR_125367.1 | n.77-10793T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH8 | ENST00000403437.2 | c.4740A>C | p.Ala1580= | synonymous_variant | 34/40 | 5 | NM_002472.3 | P1 | |
ENST00000399342.6 | n.77-10793T>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
ENST00000581304.1 | n.53-10793T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00317 AC: 482AN: 152194Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000819 AC: 206AN: 251426Hom.: 1 AF XY: 0.000618 AC XY: 84AN XY: 135886
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GnomAD4 exome AF: 0.000300 AC: 439AN: 1461874Hom.: 3 Cov.: 32 AF XY: 0.000253 AC XY: 184AN XY: 727232
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GnomAD4 genome ? AF: 0.00316 AC: 482AN: 152312Hom.: 2 Cov.: 32 AF XY: 0.00317 AC XY: 236AN XY: 74484
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 02, 2015 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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