NM_002474.3:c.4239C>T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_002474.3(MYH11):c.4239C>T(p.Ala1413Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000428 in 1,614,148 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002474.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH11 | NM_002474.3 | c.4239C>T | p.Ala1413Ala | synonymous_variant | Exon 31 of 41 | ENST00000300036.6 | NP_002465.1 | |
MYH11 | NM_001040113.2 | c.4260C>T | p.Ala1420Ala | synonymous_variant | Exon 32 of 43 | ENST00000452625.7 | NP_001035202.1 | |
NDE1 | NM_017668.3 | c.*36G>A | 3_prime_UTR_variant | Exon 9 of 9 | ENST00000396354.6 | NP_060138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH11 | ENST00000300036.6 | c.4239C>T | p.Ala1413Ala | synonymous_variant | Exon 31 of 41 | 1 | NM_002474.3 | ENSP00000300036.5 | ||
MYH11 | ENST00000452625.7 | c.4260C>T | p.Ala1420Ala | synonymous_variant | Exon 32 of 43 | 1 | NM_001040113.2 | ENSP00000407821.2 | ||
NDE1 | ENST00000396354.6 | c.*36G>A | 3_prime_UTR_variant | Exon 9 of 9 | 1 | NM_017668.3 | ENSP00000379642.1 |
Frequencies
GnomAD3 genomes AF: 0.00225 AC: 343AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000592 AC: 149AN: 251478Hom.: 1 AF XY: 0.000441 AC XY: 60AN XY: 135914
GnomAD4 exome AF: 0.000237 AC: 347AN: 1461884Hom.: 1 Cov.: 72 AF XY: 0.000202 AC XY: 147AN XY: 727240
GnomAD4 genome AF: 0.00226 AC: 344AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.00220 AC XY: 164AN XY: 74444
ClinVar
Submissions by phenotype
not specified Benign:5
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Familial thoracic aortic aneurysm and aortic dissection Benign:4
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This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
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not provided Benign:2
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Aortic aneurysm, familial thoracic 4 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at