8-68055838-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_024870.4(PREX2):c.1102T>G(p.Leu368Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,610,610 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 (★).
Frequency
Consequence
NM_024870.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PREX2 | NM_024870.4 | c.1102T>G | p.Leu368Val | missense_variant | 10/40 | ENST00000288368.5 | |
PREX2 | NM_025170.6 | c.1102T>G | p.Leu368Val | missense_variant | 10/24 | ||
PREX2 | XM_047422267.1 | c.967T>G | p.Leu323Val | missense_variant | 10/40 | ||
PREX2 | XM_047422268.1 | c.1102T>G | p.Leu368Val | missense_variant | 10/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PREX2 | ENST00000288368.5 | c.1102T>G | p.Leu368Val | missense_variant | 10/40 | 1 | NM_024870.4 | P1 | |
PREX2 | ENST00000529398.5 | n.1129T>G | non_coding_transcript_exon_variant | 10/24 | 1 | ||||
PREX2 | ENST00000517617.1 | n.813T>G | non_coding_transcript_exon_variant | 8/24 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247278Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133474
GnomAD4 exome AF: 0.0000336 AC: 49AN: 1458500Hom.: 0 Cov.: 30 AF XY: 0.0000331 AC XY: 24AN XY: 725462
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2022 | The c.1102T>G (p.L368V) alteration is located in exon 10 (coding exon 10) of the PREX2 gene. This alteration results from a T to G substitution at nucleotide position 1102, causing the leucine (L) at amino acid position 368 to be replaced by a valine (V). 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