15-48201415-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145668.2(CTXN2):āc.115A>Gā(p.Ile39Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000362 in 1,551,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001145668.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000228 AC: 35AN: 153802Hom.: 0 AF XY: 0.000159 AC XY: 13AN XY: 81602
GnomAD4 exome AF: 0.000379 AC: 530AN: 1399114Hom.: 0 Cov.: 31 AF XY: 0.000361 AC XY: 249AN XY: 690080
GnomAD4 genome AF: 0.000204 AC: 31AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.115A>G (p.I39V) alteration is located in exon 2 (coding exon 1) of the CTXN2 gene. This alteration results from a A to G substitution at nucleotide position 115, causing the isoleucine (I) at amino acid position 39 to be replaced by a valine (V). 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