chr11-72868025-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014824.3(FCHSD2):āc.1148T>Cā(p.Ile383Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000215 in 1,554,690 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014824.3 missense, splice_region
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.1148T>C | p.Ile383Thr | missense_variant, splice_region_variant | 13/20 | ENST00000409418.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCHSD2 | ENST00000409418.9 | c.1148T>C | p.Ile383Thr | missense_variant, splice_region_variant | 13/20 | 2 | NM_014824.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 26AN: 163996Hom.: 0 AF XY: 0.000152 AC XY: 13AN XY: 85584
GnomAD4 exome AF: 0.000212 AC: 298AN: 1402354Hom.: 1 Cov.: 30 AF XY: 0.000218 AC XY: 151AN XY: 691778
GnomAD4 genome AF: 0.000236 AC: 36AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2024 | The c.1148T>C (p.I383T) alteration is located in exon 13 (coding exon 13) of the FCHSD2 gene. This alteration results from a T to C substitution at nucleotide position 1148, causing the isoleucine (I) at amino acid position 383 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