X-93671996-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004538.6(NAP1L3):c.1309G>A(p.Ala437Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000566 in 1,202,127 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 33 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 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. A437G) has been classified as Benign.
Frequency
Consequence
NM_004538.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000117 AC: 13AN: 111424Hom.: 0 Cov.: 22 AF XY: 0.000208 AC XY: 7AN XY: 33586
GnomAD3 exomes AF: 0.0000840 AC: 14AN: 166625Hom.: 0 AF XY: 0.000131 AC XY: 7AN XY: 53591
GnomAD4 exome AF: 0.0000504 AC: 55AN: 1090703Hom.: 0 Cov.: 31 AF XY: 0.0000728 AC XY: 26AN XY: 357145
GnomAD4 genome AF: 0.000117 AC: 13AN: 111424Hom.: 0 Cov.: 22 AF XY: 0.000208 AC XY: 7AN XY: 33586
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1309G>A (p.A437T) alteration is located in exon 1 (coding exon 1) of the NAP1L3 gene. This alteration results from a G to A substitution at nucleotide position 1309, causing the alanine (A) at amino acid position 437 to be replaced by a threonine (T). 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