5-72990773-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_138782.3(FCHO2):c.404C>T(p.Ala135Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,555,398 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_138782.3 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 |
---|---|---|---|---|---|---|---|---|---|---|
FCHO2 | ENST00000430046.7 | c.404C>T | p.Ala135Val | missense_variant | Exon 5 of 26 | 1 | NM_138782.3 | ENSP00000393776.2 | ||
FCHO2 | ENST00000287761.7 | c.404C>T | p.Ala135Val | missense_variant | Exon 5 of 11 | 1 | ENSP00000287761.6 | |||
FCHO2 | ENST00000512348.5 | c.404C>T | p.Ala135Val | missense_variant | Exon 5 of 25 | 2 | ENSP00000427296.1 | |||
FCHO2 | ENST00000507345.6 | c.329C>T | p.Ala110Val | missense_variant | Exon 4 of 7 | 5 | ENSP00000426842.2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152058Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000855 AC: 14AN: 163690Hom.: 0 AF XY: 0.0000813 AC XY: 7AN XY: 86126
GnomAD4 exome AF: 0.0000150 AC: 21AN: 1403340Hom.: 0 Cov.: 31 AF XY: 0.0000173 AC XY: 12AN XY: 692390
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152058Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.404C>T (p.A135V) alteration is located in exon 5 (coding exon 5) of the FCHO2 gene. This alteration results from a C to T substitution at nucleotide position 404, causing the alanine (A) at amino acid position 135 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