2-87753614-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_002665.4(PLGLB2):c.272C>A(p.Ala91Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002665.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLGLB2 | ENST00000359481.9 | c.272C>A | p.Ala91Glu | missense_variant | Exon 3 of 4 | 1 | NM_002665.4 | ENSP00000352458.4 | ||
PLGLB2 | ENST00000465361.1 | n.1243C>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 1 | |||||
PLGLB2 | ENST00000410086.3 | n.272C>A | non_coding_transcript_exon_variant | Exon 3 of 5 | 3 | ENSP00000386317.3 | ||||
NCAL1 | ENST00000646855.1 | n.2809C>A | non_coding_transcript_exon_variant | Exon 20 of 22 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 346AN: 120114Hom.: 17 Cov.: 17 FAILED QC
GnomAD3 exomes AF: 0.00160 AC: 87AN: 54334Hom.: 0 AF XY: 0.00149 AC XY: 41AN XY: 27546
GnomAD4 exome AF: 0.00215 AC: 1077AN: 500116Hom.: 49 Cov.: 0 AF XY: 0.00183 AC XY: 498AN XY: 272596
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00288 AC: 346AN: 120204Hom.: 17 Cov.: 17 AF XY: 0.00377 AC XY: 215AN XY: 57004
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.272C>A (p.A91E) alteration is located in exon 3 (coding exon 3) of the PLGLB2 gene. This alteration results from a C to A substitution at nucleotide position 272, causing the alanine (A) at amino acid position 91 to be replaced by a glutamic acid (E). 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