rs34689457
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_024782.3(NHEJ1):c.40G>T(p.Ala14Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A14T) has been classified as Benign.
Frequency
Consequence
NM_024782.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NHEJ1 | NM_024782.3 | c.40G>T | p.Ala14Ser | missense_variant | 2/8 | ENST00000356853.10 | NP_079058.1 | |
NHEJ1 | NM_001377499.1 | c.40G>T | p.Ala14Ser | missense_variant | 2/8 | NP_001364428.1 | ||
NHEJ1 | NM_001377498.1 | c.40G>T | p.Ala14Ser | missense_variant | 2/8 | NP_001364427.1 | ||
NHEJ1 | NR_165304.1 | n.136G>T | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHEJ1 | ENST00000356853.10 | c.40G>T | p.Ala14Ser | missense_variant | 2/8 | 1 | NM_024782.3 | ENSP00000349313.5 | ||
ENSG00000280537 | ENST00000318673.6 | n.*1162G>T | non_coding_transcript_exon_variant | 11/17 | 2 | ENSP00000320919.3 | ||||
ENSG00000280537 | ENST00000318673.6 | n.*1162G>T | 3_prime_UTR_variant | 11/17 | 2 | ENSP00000320919.3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251424Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135892
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461890Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at