rs772663614
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS2
The NM_001943.5(DSG2):c.15G>A(p.Pro5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 151,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P5P) has been classified as Likely benign.
Frequency
Consequence
NM_001943.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSG2 | NM_001943.5 | c.15G>A | p.Pro5= | synonymous_variant | 1/15 | ENST00000261590.13 | |
DSG2 | XM_047437315.1 | c.-558G>A | 5_prime_UTR_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSG2 | ENST00000261590.13 | c.15G>A | p.Pro5= | synonymous_variant | 1/15 | 1 | NM_001943.5 | P1 | |
DSG2 | ENST00000683654.1 | c.15G>A | p.Pro5= | synonymous_variant | 1/7 | ||||
DSG2 | ENST00000682241.2 | c.15G>A | p.Pro5= | synonymous_variant | 1/7 | ||||
DSG2 | ENST00000585206.1 | c.15G>A | p.Pro5= | synonymous_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151962Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1110678Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 528424
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 151962Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74242
ClinVar
Submissions by phenotype
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at