chr17-45240621-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005892.4(FMNL1):c.1226C>T(p.Ala409Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000292 in 1,612,920 control chromosomes in the GnomAD database, including 3 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 Uncertain significance (★).
Frequency
Consequence
NM_005892.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FMNL1 | NM_005892.4 | c.1226C>T | p.Ala409Val | missense_variant | Exon 12 of 27 | ENST00000331495.8 | NP_005883.3 | |
FMNL1 | NM_001411128.1 | c.1226C>T | p.Ala409Val | missense_variant | Exon 12 of 26 | NP_001398057.1 | ||
FMNL1-AS1 | NR_186807.1 | n.825+325G>A | intron_variant | Intron 1 of 1 | ||||
FMNL1-AS1 | NR_186808.1 | n.661-17G>A | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000525 AC: 131AN: 249588Hom.: 0 AF XY: 0.000697 AC XY: 94AN XY: 134908
GnomAD4 exome AF: 0.000305 AC: 445AN: 1460606Hom.: 3 Cov.: 31 AF XY: 0.000398 AC XY: 289AN XY: 726568
GnomAD4 genome AF: 0.000171 AC: 26AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1226C>T (p.A409V) alteration is located in exon 12 (coding exon 12) of the FMNL1 gene. This alteration results from a C to T substitution at nucleotide position 1226, causing the alanine (A) at amino acid position 409 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