16-1770766-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_002513.3(NME3):c.393G>A(p.Lys131Lys) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000621 in 1,449,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002513.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NME3 | NM_002513.3 | c.393G>A | p.Lys131Lys | splice_region_variant, synonymous_variant | Exon 5 of 5 | ENST00000219302.8 | NP_002504.2 | |
NME3 | XM_005255332.5 | c.385G>A | p.Glu129Lys | missense_variant, splice_region_variant | Exon 5 of 5 | XP_005255389.1 | ||
NME3 | XM_011522504.3 | c.404G>A | p.Arg135Lys | missense_variant, splice_region_variant | Exon 5 of 5 | XP_011520806.1 | ||
NME3 | XM_011522503.3 | c.396G>A | p.Arg132Arg | splice_region_variant, synonymous_variant | Exon 5 of 5 | XP_011520805.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000882 AC: 2AN: 226802Hom.: 0 AF XY: 0.00000800 AC XY: 1AN XY: 124962
GnomAD4 exome AF: 0.00000621 AC: 9AN: 1449830Hom.: 0 Cov.: 31 AF XY: 0.00000555 AC XY: 4AN XY: 720460
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at