2-20204237-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002997.5(SDC1):c.203C>T(p.Thr68Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0032 in 1,593,916 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002997.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00309 AC: 454AN: 147080Hom.: 4 Cov.: 30
GnomAD3 exomes AF: 0.00531 AC: 1266AN: 238300Hom.: 14 AF XY: 0.00542 AC XY: 704AN XY: 129854
GnomAD4 exome AF: 0.00321 AC: 4643AN: 1446716Hom.: 36 Cov.: 38 AF XY: 0.00345 AC XY: 2487AN XY: 720110
GnomAD4 genome AF: 0.00308 AC: 454AN: 147200Hom.: 4 Cov.: 30 AF XY: 0.00296 AC XY: 213AN XY: 71920
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at