12-54644751-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_053283.4(DCD):c.295G>A(p.Val99Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000318 in 1,604,394 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_053283.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCD | ENST00000293371.11 | c.295G>A | p.Val99Ile | missense_variant | Exon 5 of 5 | 1 | NM_053283.4 | ENSP00000293371.6 | ||
DCD | ENST00000456047.2 | c.359G>A | p.Arg120His | missense_variant | Exon 6 of 6 | 1 | ENSP00000406773.2 | |||
DCD | ENST00000546807.5 | n.*228G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 1 | ENSP00000450415.1 | ||||
DCD | ENST00000546807.5 | n.*228G>A | 3_prime_UTR_variant | Exon 6 of 6 | 1 | ENSP00000450415.1 |
Frequencies
GnomAD3 genomes AF: 0.0000402 AC: 6AN: 149240Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000626 AC: 15AN: 239750Hom.: 0 AF XY: 0.0000773 AC XY: 10AN XY: 129372
GnomAD4 exome AF: 0.0000309 AC: 45AN: 1455044Hom.: 0 Cov.: 33 AF XY: 0.0000387 AC XY: 28AN XY: 723250
GnomAD4 genome AF: 0.0000402 AC: 6AN: 149350Hom.: 0 Cov.: 29 AF XY: 0.0000413 AC XY: 3AN XY: 72706
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