7-134933235-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_033138.4(CALD1):c.466C>T(p.Arg156Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,607,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033138.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000674 AC: 1AN: 148442Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000408 AC: 10AN: 245184Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 132890
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1458612Hom.: 0 Cov.: 33 AF XY: 0.0000152 AC XY: 11AN XY: 725420
GnomAD4 genome AF: 0.00000673 AC: 1AN: 148560Hom.: 0 Cov.: 29 AF XY: 0.0000138 AC XY: 1AN XY: 72302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.466C>T (p.R156C) alteration is located in exon 5 (coding exon 3) of the CALD1 gene. This alteration results from a C to T substitution at nucleotide position 466, causing the arginine (R) at amino acid position 156 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at