15-41850903-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_016642.4(SPTBN5):c.10872G>A(p.Pro3624Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,603,940 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_016642.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPTBN5 | NM_016642.4 | c.10872G>A | p.Pro3624Pro | synonymous_variant | Exon 66 of 68 | ENST00000320955.8 | NP_057726.4 | |
SPTBN5 | XM_017022299.2 | c.11052G>A | p.Pro3684Pro | synonymous_variant | Exon 64 of 66 | XP_016877788.1 | ||
SPTBN5 | XM_017022302.2 | c.8229G>A | p.Pro2743Pro | synonymous_variant | Exon 52 of 54 | XP_016877791.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000605 AC: 14AN: 231558Hom.: 0 AF XY: 0.0000636 AC XY: 8AN XY: 125762
GnomAD4 exome AF: 0.000116 AC: 168AN: 1451780Hom.: 1 Cov.: 30 AF XY: 0.000129 AC XY: 93AN XY: 721112
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74326
ClinVar
Submissions by phenotype
SPTBN5-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