chr7-29884143-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080529.3(WIPF3):c.649C>T(p.Pro217Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00019 in 1,524,316 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P217H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001080529.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WIPF3 | NM_001080529.3 | c.649C>T | p.Pro217Ser | missense_variant | 5/9 | ENST00000242140.10 | |
WIPF3 | NM_001391973.1 | c.649C>T | p.Pro217Ser | missense_variant | 5/8 | ||
WIPF3 | XM_017012522.2 | c.616C>T | p.Pro206Ser | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WIPF3 | ENST00000242140.10 | c.649C>T | p.Pro217Ser | missense_variant | 5/9 | 5 | NM_001080529.3 | P5 | |
WIPF3 | ENST00000409123.5 | c.649C>T | p.Pro217Ser | missense_variant | 5/8 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000534 AC: 8AN: 149824Hom.: 0 Cov.: 23
GnomAD3 exomes AF: 0.0000645 AC: 8AN: 124068Hom.: 0 AF XY: 0.0000753 AC XY: 5AN XY: 66364
GnomAD4 exome AF: 0.000204 AC: 281AN: 1374404Hom.: 0 Cov.: 36 AF XY: 0.000176 AC XY: 119AN XY: 676152
GnomAD4 genome AF: 0.0000534 AC: 8AN: 149912Hom.: 0 Cov.: 23 AF XY: 0.0000821 AC XY: 6AN XY: 73096
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.649C>T (p.P217S) alteration is located in exon 5 (coding exon 4) of the WIPF3 gene. This alteration results from a C to T substitution at nucleotide position 649, causing the proline (P) at amino acid position 217 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