chr15-34793480-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001406485.1(ACTC1):c.-170C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001406485.1 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000362 AC: 55AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251472Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135916
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727248
GnomAD4 genome AF: 0.000361 AC: 55AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000323 AC XY: 24AN XY: 74406
ClinVar
Submissions by phenotype
not specified Benign:3
- -
- -
Variant summary: The ACTC1 c.219C>T (p.Ile73Ile) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Though one in silico tool predicts a damaging outcome for this variant, 5/5 splice prediction tools predict no significant impact on normal splicing, as well as ESE finder predicts that this variant doesnt affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 33/277206 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.000999 (24/24022). This frequency is about 40 times the estimated maximal expected allele frequency of a pathogenic ACTC1 variant (0.000025), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, one clinical diagnostic laboratory classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign. -
not provided Benign:3
- -
- -
- -
Cardiomyopathy Benign:2
- -
- -
Hypertrophic cardiomyopathy 11;C2748552:Atrial septal defect 5;C3150681:Dilated cardiomyopathy 1R Benign:1
- -
Hypertrophic cardiomyopathy Benign:1
- -
Cardiovascular phenotype Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at