chr2-223984765-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001136528.2(SERPINE2):c.871G>T(p.Val291Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000868 in 1,612,574 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001136528.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINE2 | NM_001136528.2 | c.871G>T | p.Val291Leu | missense_variant | 5/9 | ENST00000409304.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINE2 | ENST00000409304.6 | c.871G>T | p.Val291Leu | missense_variant | 5/9 | 1 | NM_001136528.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000799 AC: 20AN: 250442Hom.: 0 AF XY: 0.0000960 AC XY: 13AN XY: 135364
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1460256Hom.: 1 Cov.: 31 AF XY: 0.0000936 AC XY: 68AN XY: 726434
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | The c.907G>T (p.V303L) alteration is located in exon 5 (coding exon 5) of the SERPINE2 gene. This alteration results from a G to T substitution at nucleotide position 907, causing the valine (V) at amino acid position 303 to be replaced by a leucine (L). 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