14-100149483-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_206918.3(DEGS2):c.310C>T(p.Arg104Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000077 in 1,598,226 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_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.310C>T | p.Arg104Cys | missense_variant | 2/3 | ENST00000305631.7 | |
DEGS2 | XM_006720043.4 | c.202C>T | p.Arg68Cys | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEGS2 | ENST00000305631.7 | c.310C>T | p.Arg104Cys | missense_variant | 2/3 | 1 | NM_206918.3 | P1 | |
DEGS2 | ENST00000553834.1 | c.83-2576C>T | intron_variant | 3 | |||||
DEGS2 | ENST00000557117.1 | n.342C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152258Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.000140 AC: 31AN: 221126Hom.: 0 AF XY: 0.000149 AC XY: 18AN XY: 120816
GnomAD4 exome AF: 0.0000768 AC: 111AN: 1445850Hom.: 0 Cov.: 38 AF XY: 0.0000822 AC XY: 59AN XY: 718020
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152376Hom.: 0 Cov.: 35 AF XY: 0.0000805 AC XY: 6AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.310C>T (p.R104C) alteration is located in exon 2 (coding exon 2) of the DEGS2 gene. This alteration results from a C to T substitution at nucleotide position 310, causing the arginine (R) at amino acid position 104 to be replaced by a cysteine (C). 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