12-122753750-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003677.5(DENR):c.49C>T(p.Pro17Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,461,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003677.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DENR | NM_003677.5 | c.49C>T | p.Pro17Ser | missense_variant | Exon 2 of 8 | ENST00000280557.11 | NP_003668.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DENR | ENST00000280557.11 | c.49C>T | p.Pro17Ser | missense_variant | Exon 2 of 8 | 1 | NM_003677.5 | ENSP00000280557.6 | ||
DENR | ENST00000455982.2 | c.49C>T | p.Pro17Ser | missense_variant | Exon 2 of 8 | 5 | ENSP00000413661.2 | |||
DENR | ENST00000537955.1 | n.162C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
DENR | ENST00000539463.1 | n.182C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249234Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135220
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461702Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 727132
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
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