rs201260899
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005218.4(DEFB1):c.131G>T(p.Cys44Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C44Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_005218.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEFB1 | ENST00000297439.4 | c.131G>T | p.Cys44Phe | missense_variant | Exon 2 of 2 | 1 | NM_005218.4 | ENSP00000297439.3 | ||
GS1-24F4.2 | ENST00000531701.1 | n.226-14365C>A | intron_variant | Intron 2 of 2 | 3 | |||||
GS1-24F4.2 | ENST00000655804.1 | n.323-2424C>A | intron_variant | Intron 2 of 2 | ||||||
GS1-24F4.2 | ENST00000657010.1 | n.*119C>A | downstream_gene_variant |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251464Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135908
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at