4-17515466-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001079827.2(CLRN2):c.200G>A(p.Arg67Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,613,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001079827.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLRN2 | NM_001079827.2 | c.200G>A | p.Arg67Gln | missense_variant | 1/3 | ENST00000511148.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLRN2 | ENST00000511148.2 | c.200G>A | p.Arg67Gln | missense_variant | 1/3 | 1 | NM_001079827.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000113 AC: 28AN: 246888Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 134188
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461694Hom.: 0 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 727128
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.200G>A (p.R67Q) alteration is located in exon 1 (coding exon 1) of the CLRN2 gene. This alteration results from a G to A substitution at nucleotide position 200, causing the arginine (R) at amino acid position 67 to be replaced by a glutamine (Q). 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