chr20-33064825-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001376932.3(BPIFB3):c.892A>C(p.Met298Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001376932.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BPIFB3 | NM_001376932.3 | c.892A>C | p.Met298Leu | missense_variant | 9/16 | ENST00000375494.4 | |
BPIFB3 | NM_182658.5 | c.892A>C | p.Met298Leu | missense_variant | 8/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPIFB3 | ENST00000375494.4 | c.892A>C | p.Met298Leu | missense_variant | 9/16 | 1 | NM_001376932.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152124Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249872Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135102
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461014Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 726840
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.904A>C (p.M302L) alteration is located in exon 8 (coding exon 8) of the BPIFB3 gene. This alteration results from a A to C substitution at nucleotide position 904, causing the methionine (M) at amino acid position 302 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