chr4-17515502-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001079827.2(CLRN2):c.236G>T(p.Arg79Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,613,776 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R79C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001079827.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLRN2 | NM_001079827.2 | c.236G>T | p.Arg79Leu | missense_variant | 1/3 | ENST00000511148.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLRN2 | ENST00000511148.2 | c.236G>T | p.Arg79Leu | missense_variant | 1/3 | 1 | NM_001079827.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000812 AC: 20AN: 246416Hom.: 0 AF XY: 0.0000822 AC XY: 11AN XY: 133890
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461568Hom.: 0 Cov.: 34 AF XY: 0.0000536 AC XY: 39AN XY: 727054
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74416
ClinVar
Submissions by phenotype
Hearing loss, autosomal recessive 117 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | 3billion | Jan 03, 2022 | The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000076, PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.765, PP3_P). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at