16-15703972-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_002474.3(MYH11):c.*19G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00022 in 1,613,786 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 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH11 | NM_002474.3 | c.*19G>A | 3_prime_UTR_variant | Exon 41 of 41 | ENST00000300036.6 | NP_002465.1 | ||
MYH11 | NM_001040113.2 | c.*160G>A | 3_prime_UTR_variant | Exon 43 of 43 | ENST00000452625.7 | NP_001035202.1 | ||
NDE1 | NM_017668.3 | c.947+7112C>T | intron_variant | Intron 8 of 8 | ENST00000396354.6 | NP_060138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH11 | ENST00000300036 | c.*19G>A | 3_prime_UTR_variant | Exon 41 of 41 | 1 | NM_002474.3 | ENSP00000300036.5 | |||
MYH11 | ENST00000452625 | c.*160G>A | 3_prime_UTR_variant | Exon 43 of 43 | 1 | NM_001040113.2 | ENSP00000407821.2 | |||
NDE1 | ENST00000396354.6 | c.947+7112C>T | intron_variant | Intron 8 of 8 | 1 | NM_017668.3 | ENSP00000379642.1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 151934Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251484Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135918
GnomAD4 exome AF: 0.000225 AC: 329AN: 1461734Hom.: 1 Cov.: 31 AF XY: 0.000230 AC XY: 167AN XY: 727158
GnomAD4 genome AF: 0.000171 AC: 26AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74318
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at