1-117623314-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_017709.4(TENT5C):c.446C>T(p.Thr149Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000385 in 1,614,188 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000314 AC: 79AN: 251298Hom.: 0 AF XY: 0.000390 AC XY: 53AN XY: 135798
GnomAD4 exome AF: 0.000401 AC: 586AN: 1461892Hom.: 2 Cov.: 36 AF XY: 0.000454 AC XY: 330AN XY: 727248
GnomAD4 genome AF: 0.000230 AC: 35AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.446C>T (p.T149I) 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 446, causing the threonine (T) at amino acid position 149 to be replaced by an isoleucine (I). 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