1-37998048-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.416G>A(p.Arg139His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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.416G>A | p.Arg139His | missense_variant | Exon 4 of 6 | 1 | NM_004468.5 | ENSP00000362107.3 | ||
FHL3 | ENST00000485803.5 | n.406G>A | non_coding_transcript_exon_variant | Exon 3 of 5 | 1 | |||||
FHL3 | ENST00000477194.5 | n.604G>A | non_coding_transcript_exon_variant | Exon 4 of 6 | 2 | |||||
FHL3 | ENST00000475084.5 | n.322-178G>A | intron_variant | Intron 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251228Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135850
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461840Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 727228
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.416G>A (p.R139H) alteration is located in exon 4 (coding exon 3) of the FHL3 gene. This alteration results from a G to A substitution at nucleotide position 416, causing the arginine (R) at amino acid position 139 to be replaced by a histidine (H). 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