4-9444586-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001040448.3(DEFB131A):c.53C>T(p.Pro18Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,577,836 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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. P18S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001040448.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000673 AC: 8AN: 118910Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000591 AC: 14AN: 236908Hom.: 0 AF XY: 0.0000854 AC XY: 11AN XY: 128748
GnomAD4 exome AF: 0.000113 AC: 165AN: 1458926Hom.: 0 Cov.: 29 AF XY: 0.0000937 AC XY: 68AN XY: 725780
GnomAD4 genome AF: 0.0000673 AC: 8AN: 118910Hom.: 1 Cov.: 33 AF XY: 0.0000348 AC XY: 2AN XY: 57528
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.53C>T (p.P18L) alteration is located in exon 1 (coding exon 1) of the DEFB131 gene. This alteration results from a C to T substitution at nucleotide position 53, causing the proline (P) at amino acid position 18 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