6-159214977-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_032532.3(FNDC1):c.493C>T(p.Arg165Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,613,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R165H) has been classified as Uncertain significance.
Frequency
Consequence
NM_032532.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FNDC1 | NM_032532.3 | c.493C>T | p.Arg165Cys | missense_variant | Exon 5 of 23 | ENST00000297267.14 | NP_115921.2 | |
FNDC1 | XM_011536190.3 | c.424C>T | p.Arg142Cys | missense_variant | Exon 4 of 22 | XP_011534492.1 | ||
FNDC1 | XM_011536191.3 | c.142C>T | p.Arg48Cys | missense_variant | Exon 2 of 20 | XP_011534493.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FNDC1 | ENST00000297267.14 | c.493C>T | p.Arg165Cys | missense_variant | Exon 5 of 23 | 1 | NM_032532.3 | ENSP00000297267.9 | ||
FNDC1 | ENST00000329629.8 | c.367C>T | p.Arg123Cys | missense_variant | Exon 4 of 21 | 1 | ENSP00000333297.8 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249178Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135186
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461668Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727116
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.493C>T (p.R165C) alteration is located in exon 5 (coding exon 5) of the FNDC1 gene. This alteration results from a C to T substitution at nucleotide position 493, causing the arginine (R) at amino acid position 165 to be replaced by a cysteine (C). 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