rs4802666
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001145809.2(MYH14):c.562+46G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 1,597,016 control chromosomes in the GnomAD database, including 78,002 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5147 hom., cov: 31)
Exomes 𝑓: 0.31 ( 72855 hom. )
Consequence
MYH14
NM_001145809.2 intron
NM_001145809.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.420
Genes affected
MYH14 (HGNC:23212): (myosin heavy chain 14) This gene encodes a member of the myosin superfamily. The protein represents a conventional non-muscle myosin; it should not be confused with the unconventional myosin-14 (MYO14). Myosins are actin-dependent motor proteins with diverse functions including regulation of cytokinesis, cell motility, and cell polarity. Mutations in this gene result in one form of autosomal dominant hearing impairment. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 19-50217817-G-A is Benign according to our data. Variant chr19-50217817-G-A is described in ClinVar as [Benign]. Clinvar id is 1295265.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH14 | NM_001145809.2 | c.562+46G>A | intron_variant | ENST00000642316.2 | |||
MYH14 | NM_001077186.2 | c.562+46G>A | intron_variant | ||||
MYH14 | NM_024729.4 | c.562+46G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH14 | ENST00000642316.2 | c.562+46G>A | intron_variant | NM_001145809.2 |
Frequencies
GnomAD3 genomes ? AF: 0.246 AC: 37443AN: 151944Hom.: 5142 Cov.: 31
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GnomAD3 exomes AF: 0.282 AC: 66054AN: 234006Hom.: 9990 AF XY: 0.294 AC XY: 37716AN XY: 128092
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GnomAD4 exome AF: 0.313 AC: 451823AN: 1444954Hom.: 72855 Cov.: 33 AF XY: 0.316 AC XY: 226460AN XY: 717672
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GnomAD4 genome ? AF: 0.246 AC: 37449AN: 152062Hom.: 5147 Cov.: 31 AF XY: 0.245 AC XY: 18175AN XY: 74320
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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 | Jun 24, 2018 | - - |
Computational scores
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Name
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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