1-37997494-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004468.5(FHL3):c.754G>A(p.Ala252Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,613,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004468.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FHL3 | ENST00000373016.4 | c.754G>A | p.Ala252Thr | missense_variant | Exon 6 of 6 | 1 | NM_004468.5 | ENSP00000362107.3 | ||
FHL3 | ENST00000485803.5 | n.744G>A | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 | |||||
FHL3 | ENST00000475084.5 | n.574G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 | |||||
FHL3 | ENST00000477194.5 | n.942G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250824Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135640
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461836Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727228
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.754G>A (p.A252T) alteration is located in exon 6 (coding exon 5) of the FHL3 gene. This alteration results from a G to A substitution at nucleotide position 754, causing the alanine (A) at amino acid position 252 to be replaced by a threonine (T). 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