4-75872043-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006239.3(PPEF2):c.1631C>A(p.Thr544Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,611,294 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_006239.3 missense
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 |
---|---|---|---|---|---|---|---|
PPEF2 | NM_006239.3 | c.1631C>A | p.Thr544Lys | missense_variant | 13/17 | ENST00000286719.12 | |
PPEF2 | XM_011532039.3 | c.1631C>A | p.Thr544Lys | missense_variant | 12/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPEF2 | ENST00000286719.12 | c.1631C>A | p.Thr544Lys | missense_variant | 13/17 | 1 | NM_006239.3 | P1 | |
PPEF2 | ENST00000511880.7 | c.*1869C>A | 3_prime_UTR_variant, NMD_transcript_variant | 14/18 | 1 | ||||
PPEF2 | ENST00000652700.1 | c.194C>A | p.Thr65Lys | missense_variant | 2/6 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248518Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134204
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1459146Hom.: 0 Cov.: 29 AF XY: 0.00000964 AC XY: 7AN XY: 725800
GnomAD4 genome AF: 0.000138 AC: 21AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.1631C>A (p.T544K) alteration is located in exon 13 (coding exon 12) of the PPEF2 gene. This alteration results from a C to A substitution at nucleotide position 1631, causing the threonine (T) at amino acid position 544 to be replaced by a lysine (K). 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