NM_001159702.3:c.66G>A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001159702.3(FHL1):c.66G>A(p.Lys22Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000982 in 1,211,485 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 32 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001159702.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FHL1 | ENST00000394155.8 | c.66G>A | p.Lys22Lys | synonymous_variant | Exon 3 of 8 | 5 | NM_001159702.3 | ENSP00000377710.2 | ||
FHL1 | ENST00000370683.6 | c.114G>A | p.Lys38Lys | synonymous_variant | Exon 2 of 6 | 1 | NM_001159699.2 | ENSP00000359717.1 |
Frequencies
GnomAD3 genomes AF: 0.000557 AC: 63AN: 113187Hom.: 0 Cov.: 24 AF XY: 0.000510 AC XY: 18AN XY: 35319
GnomAD3 exomes AF: 0.000131 AC: 24AN: 183497Hom.: 0 AF XY: 0.0000589 AC XY: 4AN XY: 67931
GnomAD4 exome AF: 0.0000501 AC: 55AN: 1098243Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 13AN XY: 363597
GnomAD4 genome AF: 0.000565 AC: 64AN: 113242Hom.: 0 Cov.: 24 AF XY: 0.000537 AC XY: 19AN XY: 35384
ClinVar
Submissions by phenotype
not specified Benign:2
- -
- -
X-linked myopathy with postural muscle atrophy Benign:1
- -
not provided Benign:1
- -
FHL1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Cardiovascular phenotype Benign:1
This alteration is classified as 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