chr4-6578396-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015274.3(MAN2B2):c.289C>T(p.Arg97Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,612,630 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015274.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN2B2 | ENST00000285599.8 | c.289C>T | p.Arg97Cys | missense_variant | Exon 3 of 19 | 1 | NM_015274.3 | ENSP00000285599.3 | ||
MAN2B2 | ENST00000504248.5 | c.289C>T | p.Arg97Cys | missense_variant | Exon 3 of 19 | 2 | ENSP00000423129.1 | |||
MAN2B2 | ENST00000505907.1 | c.283C>T | p.Arg95Cys | missense_variant | Exon 3 of 17 | 2 | ENSP00000426273.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000522 AC: 13AN: 248862Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134696
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1460358Hom.: 0 Cov.: 31 AF XY: 0.0000441 AC XY: 32AN XY: 726376
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.289C>T (p.R97C) alteration is located in exon 3 (coding exon 3) of the MAN2B2 gene. This alteration results from a C to T substitution at nucleotide position 289, causing the arginine (R) at amino acid position 97 to be replaced by a cysteine (C). 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