rs74575749
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001318895.3(FHL2):c.109G>T(p.Ala37Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000333 in 1,614,160 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A37T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001318895.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FHL2 | NM_001318895.3 | c.109G>T | p.Ala37Ser | missense_variant | 3/7 | ENST00000530340.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FHL2 | ENST00000530340.6 | c.109G>T | p.Ala37Ser | missense_variant | 3/7 | 1 | NM_001318895.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00181 AC: 275AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000469 AC: 118AN: 251348Hom.: 0 AF XY: 0.000427 AC XY: 58AN XY: 135824
GnomAD4 exome AF: 0.000180 AC: 263AN: 1461840Hom.: 1 Cov.: 31 AF XY: 0.000144 AC XY: 105AN XY: 727222
GnomAD4 genome AF: 0.00181 AC: 275AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.00189 AC XY: 141AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 19, 2012 | Ala37Ser in exon 2 of FHL2: This variant is not expected to have clinical signif icance because it has been identified in 0.7% (26/3738) of African American chro mosomes from a broad population by the NHLBI Exome Sequencing Project (http://ev s.gs.washington.edu/EVS; dbSNP rs74575749). Ala37Ser in exon 2 of FHL2 (rs74575 749; allele frequency = 0.7%, 26/3738) ** - |
Primary dilated cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at