12-51269247-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001031628.2(SMAGP):c.32G>T(p.Arg11Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001031628.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMAGP | NM_001031628.2 | c.32G>T | p.Arg11Ile | missense_variant, splice_region_variant | Exon 2 of 4 | ENST00000603798.6 | NP_001026798.1 | |
SMAGP | NM_001033873.1 | c.32G>T | p.Arg11Ile | missense_variant, splice_region_variant | Exon 2 of 4 | NP_001029045.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249258Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135222
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461590Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727092
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.32G>T (p.R11I) alteration is located in exon 2 (coding exon 1) of the SMAGP gene. This alteration results from a G to T substitution at nucleotide position 32, causing the arginine (R) at amino acid position 11 to be replaced by an isoleucine (I). 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