X-103274029-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001012979.3(TCEAL5):c.535T>C(p.Phe179Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000165 in 1,210,039 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001012979.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000358 AC: 4AN: 111770Hom.: 0 Cov.: 24 AF XY: 0.0000295 AC XY: 1AN XY: 33944
GnomAD3 exomes AF: 0.0000272 AC: 5AN: 183521Hom.: 0 AF XY: 0.0000589 AC XY: 4AN XY: 67949
GnomAD4 exome AF: 0.0000146 AC: 16AN: 1098269Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 8AN XY: 363623
GnomAD4 genome AF: 0.0000358 AC: 4AN: 111770Hom.: 0 Cov.: 24 AF XY: 0.0000295 AC XY: 1AN XY: 33944
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.535T>C (p.F179L) alteration is located in exon 3 (coding exon 1) of the TCEAL5 gene. This alteration results from a T to C substitution at nucleotide position 535, causing the phenylalanine (F) at amino acid position 179 to be replaced by a leucine (L). 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