4-6576698-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015274.3(MAN2B2):c.259G>A(p.Val87Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015274.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN2B2 | ENST00000285599.8 | c.259G>A | p.Val87Ile | missense_variant | Exon 2 of 19 | 1 | NM_015274.3 | ENSP00000285599.3 | ||
MAN2B2 | ENST00000504248.5 | c.259G>A | p.Val87Ile | missense_variant | Exon 2 of 19 | 2 | ENSP00000423129.1 | |||
MAN2B2 | ENST00000505907.1 | c.253G>A | p.Val85Ile | missense_variant | Exon 2 of 17 | 2 | ENSP00000426273.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251232Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135880
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461638Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727136
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.259G>A (p.V87I) alteration is located in exon 2 (coding exon 2) of the MAN2B2 gene. This alteration results from a G to A substitution at nucleotide position 259, causing the valine (V) at amino acid position 87 to be replaced by an isoleucine (I). 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