3-184155641-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_004423.4(DVL3):c.6C>T(p.Gly2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,580,502 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. G2G) has been classified as Likely benign.
Frequency
Consequence
NM_004423.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DVL3 | NM_004423.4 | c.6C>T | p.Gly2= | synonymous_variant | 1/15 | ENST00000313143.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DVL3 | ENST00000313143.9 | c.6C>T | p.Gly2= | synonymous_variant | 1/15 | 1 | NM_004423.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000448 AC: 1AN: 223430Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 122346
GnomAD4 exome AF: 0.0000280 AC: 40AN: 1429310Hom.: 0 Cov.: 30 AF XY: 0.0000253 AC XY: 18AN XY: 711378
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151192Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73830
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at