11-126264502-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_003139.4(SRPRA):c.1563G>A(p.Thr521Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003139.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRPRA | NM_003139.4 | c.1563G>A | p.Thr521Thr | synonymous_variant | Exon 12 of 14 | ENST00000332118.11 | NP_003130.2 | |
SRPRA | NM_001177842.2 | c.1479G>A | p.Thr493Thr | synonymous_variant | Exon 11 of 13 | NP_001171313.1 | ||
SRPRA | XM_047427497.1 | c.1563G>A | p.Thr521Thr | synonymous_variant | Exon 12 of 14 | XP_047283453.1 | ||
SRPRA | XM_017018179.3 | c.1563G>A | p.Thr521Thr | synonymous_variant | Exon 12 of 14 | XP_016873668.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPRA | ENST00000332118.11 | c.1563G>A | p.Thr521Thr | synonymous_variant | Exon 12 of 14 | 1 | NM_003139.4 | ENSP00000328023.5 | ||
SRPRA | ENST00000532259.1 | c.1479G>A | p.Thr493Thr | synonymous_variant | Exon 11 of 13 | 2 | ENSP00000435508.1 | |||
SRPRA | ENST00000532268.1 | n.254G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251384Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135880
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461384Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727012
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152140Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74316
ClinVar
Submissions by phenotype
SRPRA-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