10-12133298-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_018144.4(SEC61A2):c.65C>T(p.Pro22Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000387 in 1,549,698 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_018144.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151964Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246908Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133788
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1397734Hom.: 0 Cov.: 23 AF XY: 0.00000143 AC XY: 1AN XY: 698792
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151964Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.65C>T (p.P22L) alteration is located in exon 2 (coding exon 2) of the SEC61A2 gene. This alteration results from a C to T substitution at nucleotide position 65, causing the proline (P) at amino acid position 22 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