X-93671927-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004538.6(NAP1L3):c.1378G>T(p.Ala460Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000191 in 1,097,203 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. In-silico tool predicts 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.0000388 AC: 7AN: 180640Hom.: 0 AF XY: 0.0000766 AC XY: 5AN XY: 65236
GnomAD4 exome AF: 0.0000191 AC: 21AN: 1097203Hom.: 0 Cov.: 30 AF XY: 0.0000414 AC XY: 15AN XY: 362589
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1378G>T (p.A460S) alteration is located in exon 1 (coding exon 1) of the NAP1L3 gene. This alteration results from a G to T substitution at nucleotide position 1378, causing the alanine (A) at amino acid position 460 to be replaced by a serine (S). 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