chr15-43874310-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032892.5(FRMD5):c.1288G>A(p.Val430Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,614,226 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032892.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRMD5 | NM_032892.5 | c.1288G>A | p.Val430Met | missense_variant | 14/14 | ENST00000417257.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRMD5 | ENST00000417257.6 | c.1288G>A | p.Val430Met | missense_variant | 14/14 | 1 | NM_032892.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000678 AC: 17AN: 250922Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135648
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461868Hom.: 1 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 727238
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74504
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2022 | The c.1288G>A (p.V430M) alteration is located in exon 14 (coding exon 14) of the FRMD5 gene. This alteration results from a G to A substitution at nucleotide position 1288, causing the valine (V) at amino acid position 430 to be replaced by a methionine (M). 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