chr20-33036447-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_174897.2(BPIFB6):c.580C>T(p.Pro194Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,748 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. 1/1 splice prediction tools predict no significant impact on normal splicing. 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. P194L) has been classified as Uncertain significance.
Frequency
Consequence
NM_174897.2 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
BPIFB6 | NM_174897.2 | c.580C>T | p.Pro194Ser | missense_variant, splice_region_variant | 7/15 | ENST00000349552.1 | |
BPIFB6 | XM_017027663.1 | c.628C>T | p.Pro210Ser | missense_variant, splice_region_variant | 7/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPIFB6 | ENST00000349552.1 | c.580C>T | p.Pro194Ser | missense_variant, splice_region_variant | 7/15 | 1 | NM_174897.2 | P1 | |
BPIFB6 | ENST00000542375.5 | c.*627C>T | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 8/16 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459748Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726132
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.580C>T (p.P194S) alteration is located in exon 7 (coding exon 7) of the BPIFB6 gene. This alteration results from a C to T substitution at nucleotide position 580, causing the proline (P) at amino acid position 194 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
Publications
No publications associated with this variant yet.