20-38310511-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001725.3(BPI):āc.395A>Cā(p.Asp132Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000868 in 1,613,472 control chromosomes in the GnomAD database, including 1 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 (ā ).
Frequency
Consequence
NM_001725.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BPI | NM_001725.3 | c.395A>C | p.Asp132Ala | missense_variant | 4/15 | ENST00000642449.2 | NP_001716.3 | |
BPI | XM_047440393.1 | c.407A>C | p.Asp136Ala | missense_variant | 4/13 | XP_047296349.1 | ||
BPI | XM_047440394.1 | c.407A>C | p.Asp136Ala | missense_variant | 4/12 | XP_047296350.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BPI | ENST00000642449.2 | c.395A>C | p.Asp132Ala | missense_variant | 4/15 | NM_001725.3 | ENSP00000494528 | P1 | ||
BPI | ENST00000262865.9 | c.407A>C | p.Asp136Ala | missense_variant | 4/15 | 1 | ENSP00000262865 | |||
ENST00000437016.1 | n.183+15843T>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000179 AC: 45AN: 251112Hom.: 1 AF XY: 0.000162 AC XY: 22AN XY: 135720
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461268Hom.: 1 Cov.: 30 AF XY: 0.0000922 AC XY: 67AN XY: 726834
GnomAD4 genome AF: 0.000131 AC: 20AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 24, 2023 | The c.407A>C (p.D136A) alteration is located in exon 4 (coding exon 4) of the BPI gene. This alteration results from a A to C substitution at nucleotide position 407, causing the aspartic acid (D) at amino acid position 136 to be replaced by an alanine (A). 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