chr22-32453453-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_174932.3(BPIFC):c.175C>T(p.Leu59Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000554 in 1,606,286 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_174932.3 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 | UniProt |
---|---|---|---|---|---|---|---|
BPIFC | NM_174932.3 | c.175C>T | p.Leu59Phe | missense_variant | 4/17 | ENST00000300399.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPIFC | ENST00000300399.9 | c.175C>T | p.Leu59Phe | missense_variant | 4/17 | 1 | NM_174932.3 | P1 | |
BPIFC | ENST00000397450.2 | c.175C>T | p.Leu59Phe | missense_variant | 4/4 | 1 | |||
BPIFC | ENST00000397452.5 | c.175C>T | p.Leu59Phe | missense_variant | 3/16 | 5 | P1 | ||
BPIFC | ENST00000534972.4 | c.175C>T | p.Leu59Phe | missense_variant, NMD_transcript_variant | 2/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000902 AC: 22AN: 243988Hom.: 0 AF XY: 0.0000759 AC XY: 10AN XY: 131792
GnomAD4 exome AF: 0.0000543 AC: 79AN: 1454090Hom.: 0 Cov.: 30 AF XY: 0.0000553 AC XY: 40AN XY: 723070
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.175C>T (p.L59F) alteration is located in exon 2 (coding exon 2) of the BPIFC gene. This alteration results from a C to T substitution at nucleotide position 175, causing the leucine (L) at amino acid position 59 to be replaced by a phenylalanine (F). 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