19-51367458-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_152353.3(CLDND2):c.429G>A(p.Ala143Ala) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00316 in 1,597,596 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_152353.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLDND2 | ENST00000291715.5 | c.429G>A | p.Ala143Ala | splice_region_variant, synonymous_variant | Exon 3 of 4 | 1 | NM_152353.3 | ENSP00000291715.1 | ||
ENSG00000269403 | ENST00000600067.1 | n.115+428G>A | intron_variant | Intron 1 of 3 | 5 | ENSP00000469452.1 | ||||
CLDND2 | ENST00000601435.1 | c.429G>A | p.Ala143Ala | splice_region_variant, synonymous_variant | Exon 4 of 5 | 3 | ENSP00000472077.1 | |||
CLDND2 | ENST00000593841.1 | c.119-61G>A | intron_variant | Intron 2 of 2 | 5 | ENSP00000471912.1 |
Frequencies
GnomAD3 genomes AF: 0.00179 AC: 272AN: 152114Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00282 AC: 634AN: 224462Hom.: 5 AF XY: 0.00336 AC XY: 406AN XY: 120950
GnomAD4 exome AF: 0.00331 AC: 4782AN: 1445364Hom.: 20 Cov.: 31 AF XY: 0.00352 AC XY: 2524AN XY: 717474
GnomAD4 genome AF: 0.00178 AC: 271AN: 152232Hom.: 1 Cov.: 32 AF XY: 0.00181 AC XY: 135AN XY: 74408
ClinVar
Submissions by phenotype
not provided Benign:1
CLDND2: PP3, BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at