2-27217561-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_004341.5(CAD):c.10C>T(p.Leu4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000688 in 1,454,360 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. L4L) has been classified as Likely benign.
Frequency
Consequence
NM_004341.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAD | NM_004341.5 | c.10C>T | p.Leu4= | synonymous_variant | 1/44 | ENST00000264705.9 | |
CAD | NM_001306079.2 | c.10C>T | p.Leu4= | synonymous_variant | 1/43 | ||
CAD | XM_047445803.1 | c.10C>T | p.Leu4= | synonymous_variant | 1/45 | ||
CAD | XM_006712101.4 | c.10C>T | p.Leu4= | synonymous_variant | 1/44 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAD | ENST00000264705.9 | c.10C>T | p.Leu4= | synonymous_variant | 1/44 | 1 | NM_004341.5 | P1 | |
CAD | ENST00000403525.5 | c.10C>T | p.Leu4= | synonymous_variant | 1/43 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000429 AC: 1AN: 233358Hom.: 0 AF XY: 0.00000785 AC XY: 1AN XY: 127400
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1454360Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 722860
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at