3-122564516-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_138287.3(DTX3L):c.90C>A(p.Phe30Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000453 in 1,612,384 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138287.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000202 AC: 50AN: 247858Hom.: 2 AF XY: 0.000112 AC XY: 15AN XY: 134472
GnomAD4 exome AF: 0.0000466 AC: 68AN: 1460170Hom.: 2 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 726406
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.90C>A (p.F30L) alteration is located in exon 1 (coding exon 1) of the DTX3L gene. This alteration results from a C to A substitution at nucleotide position 90, causing the phenylalanine (F) at amino acid position 30 to be replaced by a leucine (L). 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