X-93671957-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004538.6(NAP1L3):c.1348A>G(p.Met450Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,096,301 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004538.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.00000562 AC: 1AN: 177953Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 62727
GnomAD4 exome AF: 0.00000274 AC: 3AN: 1096301Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 1AN XY: 361743
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1348A>G (p.M450V) alteration is located in exon 1 (coding exon 1) of the NAP1L3 gene. This alteration results from a A to G substitution at nucleotide position 1348, causing the methionine (M) at amino acid position 450 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