chr14-100149476-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_206918.3(DEGS2):c.317G>A(p.Arg106His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,594,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_206918.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEGS2 | ENST00000305631.7 | c.317G>A | p.Arg106His | missense_variant | Exon 2 of 3 | 1 | NM_206918.3 | ENSP00000307126.5 | ||
DEGS2 | ENST00000553834.1 | c.83-2569G>A | intron_variant | Intron 1 of 1 | 3 | ENSP00000450637.1 | ||||
DEGS2 | ENST00000557117.1 | n.349G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152242Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000181 AC: 4AN: 221038Hom.: 0 AF XY: 0.0000166 AC XY: 2AN XY: 120696
GnomAD4 exome AF: 0.00000901 AC: 13AN: 1442450Hom.: 0 Cov.: 38 AF XY: 0.0000140 AC XY: 10AN XY: 715646
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152242Hom.: 0 Cov.: 35 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.317G>A (p.R106H) 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 317, causing the arginine (R) at amino acid position 106 to be replaced by a histidine (H). 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