2-219158323-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024782.3(NHEJ1):c.40G>A(p.Ala14Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00784 in 1,614,152 control chromosomes in the GnomAD database, including 827 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A14V) has been classified as Uncertain significance.
Frequency
Consequence
NM_024782.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NHEJ1 | NM_024782.3 | c.40G>A | p.Ala14Thr | missense_variant | Exon 2 of 8 | ENST00000356853.10 | NP_079058.1 | |
NHEJ1 | NM_001377499.1 | c.40G>A | p.Ala14Thr | missense_variant | Exon 2 of 8 | NP_001364428.1 | ||
NHEJ1 | NM_001377498.1 | c.40G>A | p.Ala14Thr | missense_variant | Exon 2 of 8 | NP_001364427.1 | ||
NHEJ1 | NR_165304.1 | n.136G>A | non_coding_transcript_exon_variant | Exon 2 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHEJ1 | ENST00000356853.10 | c.40G>A | p.Ala14Thr | missense_variant | Exon 2 of 8 | 1 | NM_024782.3 | ENSP00000349313.5 | ||
ENSG00000280537 | ENST00000318673.6 | n.*1162G>A | non_coding_transcript_exon_variant | Exon 11 of 17 | 2 | ENSP00000320919.3 | ||||
ENSG00000280537 | ENST00000318673.6 | n.*1162G>A | 3_prime_UTR_variant | Exon 11 of 17 | 2 | ENSP00000320919.3 |
Frequencies
GnomAD3 genomes AF: 0.0412 AC: 6276AN: 152146Hom.: 440 Cov.: 31
GnomAD3 exomes AF: 0.0111 AC: 2790AN: 251424Hom.: 168 AF XY: 0.00828 AC XY: 1125AN XY: 135892
GnomAD4 exome AF: 0.00436 AC: 6368AN: 1461888Hom.: 387 Cov.: 33 AF XY: 0.00367 AC XY: 2672AN XY: 727244
GnomAD4 genome AF: 0.0413 AC: 6284AN: 152264Hom.: 440 Cov.: 31 AF XY: 0.0392 AC XY: 2916AN XY: 74454
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Cernunnos-XLF deficiency Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at