1-37998027-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_004468.5(FHL3):c.437G>T(p.Gly146Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. G146G) has been classified as Likely benign.
Frequency
Consequence
NM_004468.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FHL3 | ENST00000373016.4 | c.437G>T | p.Gly146Val | missense_variant | Exon 4 of 6 | 1 | NM_004468.5 | ENSP00000362107.3 | ||
FHL3 | ENST00000485803.5 | n.427G>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 1 | |||||
FHL3 | ENST00000477194.5 | n.625G>T | non_coding_transcript_exon_variant | Exon 4 of 6 | 2 | |||||
FHL3 | ENST00000475084.5 | n.322-157G>T | intron_variant | Intron 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251410Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135896
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461858Hom.: 0 Cov.: 34 AF XY: 0.00000550 AC XY: 4AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.437G>T (p.G146V) alteration is located in exon 4 (coding exon 3) of the FHL3 gene. This alteration results from a G to T substitution at nucleotide position 437, causing the glycine (G) at amino acid position 146 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at