2-112738876-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_152515.5(CKAP2L):c.2185C>T(p.Arg729Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00958 in 1,613,802 control chromosomes in the GnomAD database, including 120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R729H) has been classified as Benign.
Frequency
Consequence
NM_152515.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CKAP2L | NM_152515.5 | c.2185C>T | p.Arg729Cys | missense_variant | 9/9 | ENST00000302450.11 | |
NT5DC4 | NM_001393655.1 | c.1345-37G>A | intron_variant | ENST00000688554.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CKAP2L | ENST00000302450.11 | c.2185C>T | p.Arg729Cys | missense_variant | 9/9 | 1 | NM_152515.5 | P1 | |
NT5DC4 | ENST00000688554.1 | c.1345-37G>A | intron_variant | NM_001393655.1 |
Frequencies
GnomAD3 genomes AF: 0.00782 AC: 1189AN: 152122Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00932 AC: 2344AN: 251408Hom.: 23 AF XY: 0.0102 AC XY: 1386AN XY: 135874
GnomAD4 exome AF: 0.00977 AC: 14276AN: 1461562Hom.: 111 Cov.: 31 AF XY: 0.0102 AC XY: 7426AN XY: 727116
GnomAD4 genome AF: 0.00780 AC: 1188AN: 152240Hom.: 9 Cov.: 32 AF XY: 0.00768 AC XY: 572AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | May 11, 2022 | - - |
not provided Benign:1
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