14-100149447-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_206918.3(DEGS2):c.346G>A(p.Val116Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 1,597,002 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_206918.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DEGS2 | NM_206918.3 | c.346G>A | p.Val116Met | missense_variant | 2/3 | ENST00000305631.7 | |
DEGS2 | XM_006720043.4 | c.238G>A | p.Val80Met | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEGS2 | ENST00000305631.7 | c.346G>A | p.Val116Met | missense_variant | 2/3 | 1 | NM_206918.3 | P1 | |
DEGS2 | ENST00000553834.1 | c.83-2540G>A | intron_variant | 3 | |||||
DEGS2 | ENST00000557117.1 | n.378G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152260Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000306 AC: 7AN: 229024Hom.: 0 AF XY: 0.0000481 AC XY: 6AN XY: 124818
GnomAD4 exome AF: 0.0000208 AC: 30AN: 1444742Hom.: 0 Cov.: 38 AF XY: 0.0000251 AC XY: 18AN XY: 716484
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152260Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.346G>A (p.V116M) alteration is located in exon 2 (coding exon 2) of the DEGS2 gene. This alteration results from a G to A substitution at nucleotide position 346, causing the valine (V) at amino acid position 116 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