12-113399561-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006843.3(SDS):āc.148A>Gā(p.Lys50Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000309 in 1,586,324 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006843.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDS | NM_006843.3 | c.148A>G | p.Lys50Glu | missense_variant | 2/8 | ENST00000257549.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDS | ENST00000257549.9 | c.148A>G | p.Lys50Glu | missense_variant | 2/8 | 2 | NM_006843.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000237 AC: 36AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000259 AC: 58AN: 224276Hom.: 0 AF XY: 0.000222 AC XY: 27AN XY: 121488
GnomAD4 exome AF: 0.000317 AC: 454AN: 1434044Hom.: 0 Cov.: 31 AF XY: 0.000305 AC XY: 217AN XY: 710754
GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.148A>G (p.K50E) alteration is located in exon 2 (coding exon 1) of the SDS gene. This alteration results from a A to G substitution at nucleotide position 148, causing the lysine (K) at amino acid position 50 to be replaced by a glutamic acid (E). 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