1-37997478-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_004468.5(FHL3):āc.770C>Gā(p.Ser257Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,924 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 (ā ).
Frequency
Consequence
NM_004468.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FHL3 | ENST00000373016.4 | c.770C>G | p.Ser257Cys | missense_variant | Exon 6 of 6 | 1 | NM_004468.5 | ENSP00000362107.3 | ||
FHL3 | ENST00000485803.5 | n.760C>G | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 | |||||
FHL3 | ENST00000475084.5 | n.590C>G | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 | |||||
FHL3 | ENST00000477194.5 | n.958C>G | non_coding_transcript_exon_variant | Exon 6 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250976Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135696
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461836Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727232
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.770C>G (p.S257C) alteration is located in exon 6 (coding exon 5) of the FHL3 gene. This alteration results from a C to G substitution at nucleotide position 770, causing the serine (S) at amino acid position 257 to be replaced by a cysteine (C). 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