1-117623670-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_017709.4(TENT5C):c.802C>T(p.Arg268Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,938 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 (★).
Frequency
Consequence
NM_017709.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250694Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135578
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461854Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 727228
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.802C>T (p.R268C) alteration is located in exon 2 (coding exon 1) of the FAM46C gene. This alteration results from a C to T substitution at nucleotide position 802, causing the arginine (R) at amino acid position 268 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