chr20-33064701-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001376932.3(BPIFB3):c.768C>A(p.Asp256Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,614,056 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BPIFB3 | NM_001376932.3 | c.768C>A | p.Asp256Glu | missense_variant | 9/16 | ENST00000375494.4 | |
BPIFB3 | NM_182658.5 | c.768C>A | p.Asp256Glu | missense_variant | 8/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPIFB3 | ENST00000375494.4 | c.768C>A | p.Asp256Glu | missense_variant | 9/16 | 1 | NM_001376932.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000927 AC: 141AN: 152162Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.000732 AC: 184AN: 251220Hom.: 1 AF XY: 0.000707 AC XY: 96AN XY: 135768
GnomAD4 exome AF: 0.00145 AC: 2124AN: 1461776Hom.: 3 Cov.: 33 AF XY: 0.00139 AC XY: 1010AN XY: 727182
GnomAD4 genome ? AF: 0.000926 AC: 141AN: 152280Hom.: 2 Cov.: 31 AF XY: 0.000846 AC XY: 63AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2023 | The c.780C>A (p.D260E) alteration is located in exon 8 (coding exon 8) of the BPIFB3 gene. This alteration results from a C to A substitution at nucleotide position 780, causing the aspartic acid (D) at amino acid position 260 to be replaced by a glutamic acid (E). 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