4-177310069-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018248.3(NEIL3):c.116C>T(p.Ala39Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000325 in 1,598,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. 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. A39T) has been classified as Uncertain significance.
Frequency
Consequence
NM_018248.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEIL3 | ENST00000264596.4 | c.116C>T | p.Ala39Val | missense_variant | Exon 1 of 10 | 1 | NM_018248.3 | ENSP00000264596.3 | ||
NEIL3 | ENST00000513321.1 | n.116C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 1 | ENSP00000424735.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000132 AC: 3AN: 227212Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 125166
GnomAD4 exome AF: 0.0000318 AC: 46AN: 1446546Hom.: 0 Cov.: 32 AF XY: 0.0000306 AC XY: 22AN XY: 719254
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.116C>T (p.A39V) alteration is located in exon 1 (coding exon 1) of the NEIL3 gene. This alteration results from a C to T substitution at nucleotide position 116, causing the alanine (A) at amino acid position 39 to be replaced by a valine (V). 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