17-35129470-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017559.4(FNDC8):c.634C>T(p.Leu212Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017559.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FNDC8 | NM_017559.4 | c.634C>T | p.Leu212Phe | missense_variant | Exon 3 of 4 | ENST00000158009.6 | NP_060029.1 | |
NLE1 | NM_018096.5 | c.*2967G>A | 3_prime_UTR_variant | Exon 13 of 13 | ENST00000442241.9 | NP_060566.2 | ||
NLE1 | XM_017024777.2 | c.*2967G>A | 3_prime_UTR_variant | Exon 11 of 11 | XP_016880266.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FNDC8 | ENST00000158009.6 | c.634C>T | p.Leu212Phe | missense_variant | Exon 3 of 4 | 1 | NM_017559.4 | ENSP00000158009.4 | ||
NLE1 | ENST00000442241 | c.*2967G>A | 3_prime_UTR_variant | Exon 13 of 13 | 1 | NM_018096.5 | ENSP00000413572.3 | |||
NLE1 | ENST00000586869 | c.*2967G>A | 3_prime_UTR_variant | Exon 12 of 12 | 1 | ENSP00000466588.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251484Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135914
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461888Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.634C>T (p.L212F) alteration is located in exon 3 (coding exon 3) of the FNDC8 gene. This alteration results from a C to T substitution at nucleotide position 634, causing the leucine (L) at amino acid position 212 to be replaced by a phenylalanine (F). 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