19-40759540-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004596.5(SNRPA):c.356C>T(p.Pro119Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000991 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004596.5 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: 0.0000460 AC: 7AN: 152058Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251276Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135854
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461850Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727230
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152058Hom.: 0 Cov.: 31 AF XY: 0.0000808 AC XY: 6AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.356C>T (p.P119L) alteration is located in exon 3 (coding exon 3) of the SNRPA gene. This alteration results from a C to T substitution at nucleotide position 356, causing the proline (P) at amino acid position 119 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