rs6731822
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_152515.5(CKAP2L):āc.1123A>Gā(p.Ile375Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.953 in 1,614,134 control chromosomes in the GnomAD database, including 733,694 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_152515.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CKAP2L | NM_152515.5 | c.1123A>G | p.Ile375Val | missense_variant | 4/9 | ENST00000302450.11 | |
CKAP2L | NM_001304361.2 | c.628A>G | p.Ile210Val | missense_variant | 4/9 | ||
CKAP2L | XM_011510666.3 | c.628A>G | p.Ile210Val | missense_variant | 3/8 | ||
CKAP2L | NR_130712.2 | n.490-114A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CKAP2L | ENST00000302450.11 | c.1123A>G | p.Ile375Val | missense_variant | 4/9 | 1 | NM_152515.5 | P1 | |
CKAP2L | ENST00000435431.5 | c.479-114A>G | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.950 AC: 144581AN: 152164Hom.: 68703 Cov.: 31
GnomAD3 exomes AF: 0.963 AC: 242007AN: 251422Hom.: 116536 AF XY: 0.962 AC XY: 130739AN XY: 135888
GnomAD4 exome AF: 0.954 AC: 1394133AN: 1461852Hom.: 664944 Cov.: 64 AF XY: 0.954 AC XY: 694082AN XY: 727234
GnomAD4 genome ? AF: 0.950 AC: 144684AN: 152282Hom.: 68750 Cov.: 31 AF XY: 0.952 AC XY: 70863AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Filippi syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at