chr11-72887547-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014824.3(FCHSD2):c.1069G>A(p.Ala357Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000245 in 1,591,482 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_014824.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCHSD2 | NM_014824.3 | c.1069G>A | p.Ala357Thr | missense_variant | 12/20 | ENST00000409418.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCHSD2 | ENST00000409418.9 | c.1069G>A | p.Ala357Thr | missense_variant | 12/20 | 2 | NM_014824.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000348 AC: 8AN: 229672Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 124950
GnomAD4 exome AF: 0.0000118 AC: 17AN: 1439316Hom.: 0 Cov.: 29 AF XY: 0.00000978 AC XY: 7AN XY: 715800
GnomAD4 genome AF: 0.000145 AC: 22AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2023 | The c.1069G>A (p.A357T) alteration is located in exon 12 (coding exon 12) of the FCHSD2 gene. This alteration results from a G to A substitution at nucleotide position 1069, causing the alanine (A) at amino acid position 357 to be replaced by a threonine (T). 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