22-32457266-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_174932.3(BPIFC):c.121T>C(p.Tyr41His) variant causes a missense change. The variant allele was found at a frequency of 0.0000482 in 1,597,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y41C) has been classified 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BPIFC | NM_174932.3 | c.121T>C | p.Tyr41His | missense_variant | 3/17 | ENST00000300399.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPIFC | ENST00000300399.9 | c.121T>C | p.Tyr41His | missense_variant | 3/17 | 1 | NM_174932.3 | P1 | |
BPIFC | ENST00000397450.2 | c.121T>C | p.Tyr41His | missense_variant | 3/4 | 1 | |||
BPIFC | ENST00000397452.5 | c.121T>C | p.Tyr41His | missense_variant | 2/16 | 5 | P1 | ||
BPIFC | ENST00000534972.4 | c.121T>C | p.Tyr41His | missense_variant, NMD_transcript_variant | 1/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000128 AC: 3AN: 234920Hom.: 0 AF XY: 0.00000784 AC XY: 1AN XY: 127578
GnomAD4 exome AF: 0.0000498 AC: 72AN: 1445046Hom.: 0 Cov.: 31 AF XY: 0.0000528 AC XY: 38AN XY: 719078
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2023 | The c.121T>C (p.Y41H) alteration is located in exon 1 (coding exon 1) of the BPIFC gene. This alteration results from a T to C substitution at nucleotide position 121, causing the tyrosine (Y) at amino acid position 41 to be replaced by a histidine (H). 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