19-40759451-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004596.5(SNRPA):c.267C>T(p.Thr89Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000445 in 1,613,212 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004596.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00198 AC: 300AN: 151604Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000494 AC: 124AN: 250914Hom.: 0 AF XY: 0.000383 AC XY: 52AN XY: 135642
GnomAD4 exome AF: 0.000285 AC: 416AN: 1461490Hom.: 1 Cov.: 30 AF XY: 0.000265 AC XY: 193AN XY: 727050
GnomAD4 genome AF: 0.00199 AC: 302AN: 151722Hom.: 1 Cov.: 31 AF XY: 0.00200 AC XY: 148AN XY: 74070
ClinVar
Submissions by phenotype
not provided Benign:2
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SNRPA-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at