12-113398799-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006843.3(SDS):c.241G>A(p.Val81Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00186 in 1,612,552 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006843.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDS | NM_006843.3 | c.241G>A | p.Val81Ile | missense_variant | 4/8 | ENST00000257549.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDS | ENST00000257549.9 | c.241G>A | p.Val81Ile | missense_variant | 4/8 | 2 | NM_006843.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00138 AC: 210AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00145 AC: 355AN: 245454Hom.: 1 AF XY: 0.00144 AC XY: 192AN XY: 133418
GnomAD4 exome AF: 0.00191 AC: 2787AN: 1460198Hom.: 4 Cov.: 32 AF XY: 0.00183 AC XY: 1328AN XY: 726382
GnomAD4 genome ? AF: 0.00137 AC: 209AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.00129 AC XY: 96AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at