12-123466127-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_022717.4(SNRNP35):c.587C>T(p.Ser196Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,611,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S196W) has been classified as Uncertain significance.
Frequency
Consequence
NM_022717.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNRNP35 | NM_022717.4 | c.587C>T | p.Ser196Leu | missense_variant | Exon 2 of 2 | ENST00000526639.3 | NP_073208.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNRNP35 | ENST00000526639.3 | c.587C>T | p.Ser196Leu | missense_variant | Exon 2 of 2 | 1 | NM_022717.4 | ENSP00000432595.2 | ||
SNRNP35 | ENST00000412157.2 | c.602C>T | p.Ser201Leu | missense_variant | Exon 2 of 2 | 1 | ENSP00000403310.2 | |||
SNRNP35 | ENST00000527158.2 | n.99-4965C>T | intron_variant | Intron 1 of 1 | 1 | |||||
SNRNP35 | ENST00000350887.5 | c.587C>T | p.Ser196Leu | missense_variant | Exon 2 of 2 | 5 | ENSP00000340774.5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151838Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249574Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135024
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459874Hom.: 0 Cov.: 31 AF XY: 0.00000689 AC XY: 5AN XY: 726164
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151838Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74118
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.602C>T (p.S201L) alteration is located in exon 2 (coding exon 2) of the SNRNP35 gene. This alteration results from a C to T substitution at nucleotide position 602, causing the serine (S) at amino acid position 201 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