2-20203875-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002997.5(SDC1):c.565G>A(p.Glu189Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000484 in 1,611,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002997.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDC1 | NM_002997.5 | c.565G>A | p.Glu189Lys | missense_variant | 3/5 | ENST00000254351.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDC1 | ENST00000254351.9 | c.565G>A | p.Glu189Lys | missense_variant | 3/5 | 1 | NM_002997.5 | P1 | |
SDC1 | ENST00000403076.5 | c.478+87G>A | intron_variant | 1 | |||||
SDC1 | ENST00000381150.5 | c.565G>A | p.Glu189Lys | missense_variant | 4/6 | 5 | P1 | ||
SDC1 | ENST00000429035.1 | c.589G>A | p.Glu197Lys | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152162Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000684 AC: 17AN: 248604Hom.: 0 AF XY: 0.0000743 AC XY: 10AN XY: 134526
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1459328Hom.: 0 Cov.: 31 AF XY: 0.0000675 AC XY: 49AN XY: 726090
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.565G>A (p.E189K) alteration is located in exon 4 (coding exon 3) of the SDC1 gene. This alteration results from a G to A substitution at nucleotide position 565, causing the glutamic acid (E) at amino acid position 189 to be replaced by a lysine (K). 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