chr10-127892770-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152311.5(CLRN3):c.15G>T(p.Lys5Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,608,458 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_152311.5 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 |
---|---|---|---|---|---|---|---|
CLRN3 | NM_152311.5 | c.15G>T | p.Lys5Asn | missense_variant | 1/3 | ENST00000368671.4 | |
CLRN3 | XM_011539274.3 | c.15G>T | p.Lys5Asn | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLRN3 | ENST00000368671.4 | c.15G>T | p.Lys5Asn | missense_variant | 1/3 | 1 | NM_152311.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249856Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135148
GnomAD4 exome AF: 0.00000687 AC: 10AN: 1456294Hom.: 0 Cov.: 29 AF XY: 0.00000552 AC XY: 4AN XY: 724914
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 12, 2023 | The c.15G>T (p.K5N) alteration is located in exon 1 (coding exon 1) of the CLRN3 gene. This alteration results from a G to T substitution at nucleotide position 15, causing the lysine (K) at amino acid position 5 to be replaced by an asparagine (N). 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