rs118204452
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_024782.3(NHEJ1):āc.367T>Cā(p.Cys123Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. C123C) has been classified as Likely benign.
Frequency
Consequence
NM_024782.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHEJ1 | NM_024782.3 | c.367T>C | p.Cys123Arg | missense_variant | 3/8 | ENST00000356853.10 | |
NHEJ1 | NM_001377499.1 | c.367T>C | p.Cys123Arg | missense_variant | 3/8 | ||
NHEJ1 | NM_001377498.1 | c.367T>C | p.Cys123Arg | missense_variant | 3/8 | ||
NHEJ1 | NR_165304.1 | n.463T>C | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHEJ1 | ENST00000356853.10 | c.367T>C | p.Cys123Arg | missense_variant | 3/8 | 1 | NM_024782.3 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251258Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135792
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461666Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1AN XY: 727144
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cernunnos-XLF deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 27, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at