4-6575326-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015274.3(MAN2B2):āc.116T>Gā(p.Val39Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000017 in 1,585,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015274.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN2B2 | ENST00000285599.8 | c.116T>G | p.Val39Gly | missense_variant | Exon 1 of 19 | 1 | NM_015274.3 | ENSP00000285599.3 | ||
MAN2B2 | ENST00000504248.5 | c.116T>G | p.Val39Gly | missense_variant | Exon 1 of 19 | 2 | ENSP00000423129.1 | |||
MAN2B2 | ENST00000505907.1 | c.110T>G | p.Val37Gly | missense_variant | Exon 1 of 17 | 2 | ENSP00000426273.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000545 AC: 11AN: 201950Hom.: 0 AF XY: 0.0000631 AC XY: 7AN XY: 110966
GnomAD4 exome AF: 0.0000181 AC: 26AN: 1433700Hom.: 0 Cov.: 31 AF XY: 0.0000197 AC XY: 14AN XY: 711856
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.116T>G (p.V39G) alteration is located in exon 1 (coding exon 1) of the MAN2B2 gene. This alteration results from a T to G substitution at nucleotide position 116, causing the valine (V) at amino acid position 39 to be replaced by a glycine (G). 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