chr20-33068882-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001376932.3(BPIFB3):c.1046A>G(p.Asn349Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,848 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.1046A>G | p.Asn349Ser | missense_variant | 11/16 | ENST00000375494.4 | |
BPIFB3 | NM_182658.5 | c.1046A>G | p.Asn349Ser | missense_variant | 10/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPIFB3 | ENST00000375494.4 | c.1046A>G | p.Asn349Ser | missense_variant | 11/16 | 1 | NM_001376932.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152060Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251434Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135882
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461788Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 10AN XY: 727216
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152060Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.1058A>G (p.N353S) alteration is located in exon 10 (coding exon 10) of the BPIFB3 gene. This alteration results from a A to G substitution at nucleotide position 1058, causing the asparagine (N) at amino acid position 353 to be replaced by a serine (S). 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