chr20-31389161-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153323.5(DEFB119):c.131G>A(p.Arg44Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,614,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153323.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEFB119 | ENST00000376315.2 | c.131G>A | p.Arg44Gln | missense_variant | Exon 2 of 2 | 1 | ENSP00000365492.2 | |||
DEFB119 | ENST00000376321.4 | c.61+1262G>A | intron_variant | Intron 1 of 1 | 1 | NM_153289.4 | ENSP00000365499.3 | |||
DEFB119 | ENST00000339144.3 | c.61+1262G>A | intron_variant | Intron 1 of 2 | 1 | ENSP00000345768.3 | ||||
DEFB119 | ENST00000492344.1 | n.148-802G>A | intron_variant | Intron 1 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000596 AC: 15AN: 251488Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135920
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461892Hom.: 0 Cov.: 35 AF XY: 0.0000605 AC XY: 44AN XY: 727248
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.131G>A (p.R44Q) alteration is located in exon 2 (coding exon 2) of the DEFB119 gene. This alteration results from a G to A substitution at nucleotide position 131, causing the arginine (R) at amino acid position 44 to be replaced by a glutamine (Q). 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