chr20-33179620-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_080574.4(BPIFA2):c.662G>A(p.Arg221His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,612,204 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R221C) has been classified as Likely benign.
Frequency
Consequence
NM_080574.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BPIFA2 | NM_080574.4 | c.662G>A | p.Arg221His | missense_variant | 7/9 | ENST00000354932.6 | |
BPIFA2 | NM_001319164.2 | c.662G>A | p.Arg221His | missense_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPIFA2 | ENST00000354932.6 | c.662G>A | p.Arg221His | missense_variant | 7/9 | 1 | NM_080574.4 | P1 | |
BPIFA2 | ENST00000253362.6 | c.662G>A | p.Arg221His | missense_variant | 7/9 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152004Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251480Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135914
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1460082Hom.: 2 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 726454
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74366
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at