2-20202915-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002997.5(SDC1):c.784G>A(p.Val262Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,612,082 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDC1 | ENST00000254351.9 | c.784G>A | p.Val262Met | missense_variant | Exon 5 of 5 | 1 | NM_002997.5 | ENSP00000254351.4 | ||
SDC1 | ENST00000403076.5 | c.479-614G>A | intron_variant | Intron 3 of 3 | 1 | ENSP00000384613.1 | ||||
SDC1 | ENST00000381150.5 | c.784G>A | p.Val262Met | missense_variant | Exon 6 of 6 | 5 | ENSP00000370542.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247496Hom.: 0 AF XY: 0.00000747 AC XY: 1AN XY: 133936
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1459934Hom.: 0 Cov.: 32 AF XY: 0.0000317 AC XY: 23AN XY: 726082
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.784G>A (p.V262M) alteration is located in exon 6 (coding exon 5) of the SDC1 gene. This alteration results from a G to A substitution at nucleotide position 784, causing the valine (V) at amino acid position 262 to be replaced by a methionine (M). 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