rs3816208
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002998.4(SDC2):c.175G>A(p.Ala59Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 1,613,172 control chromosomes in the GnomAD database, including 5,753 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002998.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDC2 | NM_002998.4 | c.175G>A | p.Ala59Thr | missense_variant, splice_region_variant | 3/5 | ENST00000302190.9 | |
SDC2 | XM_011517212.4 | c.88G>A | p.Ala30Thr | missense_variant, splice_region_variant | 4/6 | ||
SDC2 | XM_024447228.2 | c.88G>A | p.Ala30Thr | missense_variant, splice_region_variant | 4/6 | ||
SDC2 | XM_047422076.1 | c.88G>A | p.Ala30Thr | missense_variant, splice_region_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDC2 | ENST00000302190.9 | c.175G>A | p.Ala59Thr | missense_variant, splice_region_variant | 3/5 | 1 | NM_002998.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0653 AC: 9937AN: 152126Hom.: 460 Cov.: 32
GnomAD3 exomes AF: 0.0969 AC: 24282AN: 250620Hom.: 1696 AF XY: 0.0936 AC XY: 12674AN XY: 135422
GnomAD4 exome AF: 0.0758 AC: 110741AN: 1460928Hom.: 5294 Cov.: 30 AF XY: 0.0759 AC XY: 55163AN XY: 726744
GnomAD4 genome ? AF: 0.0653 AC: 9942AN: 152244Hom.: 459 Cov.: 32 AF XY: 0.0688 AC XY: 5122AN XY: 74440
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at