20-49984115-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005985.4(SNAI1):c.374C>T(p.Ala125Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,614,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005985.4 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: 0.000263 AC: 40AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251320Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135878
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461872Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 727234
GnomAD4 genome AF: 0.000263 AC: 40AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.000363 AC XY: 27AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.374C>T (p.A125V) alteration is located in exon 2 (coding exon 2) of the SNAI1 gene. This alteration results from a C to T substitution at nucleotide position 374, causing the alanine (A) at amino acid position 125 to be replaced by a valine (V). 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