13-49145779-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001079673.2(FNDC3A):c.821C>T(p.Ala274Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000285 in 1,613,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 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 (★).
Frequency
Consequence
NM_001079673.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FNDC3A | NM_001079673.2 | c.821C>T | p.Ala274Val | missense_variant, splice_region_variant | Exon 8 of 26 | ENST00000492622.6 | NP_001073141.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250688Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135496
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460938Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726776
GnomAD4 genome AF: 0.000177 AC: 27AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.821C>T (p.A274V) alteration is located in exon 8 (coding exon 7) of the FNDC3A gene. This alteration results from a C to T substitution at nucleotide position 821, causing the alanine (A) at amino acid position 274 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