4-6578418-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015274.3(MAN2B2):c.311G>A(p.Arg104His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,450 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
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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.311G>A | p.Arg104His | missense_variant | Exon 3 of 19 | 1 | NM_015274.3 | ENSP00000285599.3 | ||
MAN2B2 | ENST00000504248.5 | c.311G>A | p.Arg104His | missense_variant | Exon 3 of 19 | 2 | ENSP00000423129.1 | |||
MAN2B2 | ENST00000505907.1 | c.305G>A | p.Arg102His | missense_variant | Exon 3 of 17 | 2 | ENSP00000426273.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250398Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135518
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461296Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 726934
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.311G>A (p.R104H) alteration is located in exon 3 (coding exon 3) of the MAN2B2 gene. This alteration results from a G to A substitution at nucleotide position 311, causing the arginine (R) at amino acid position 104 to be replaced by a histidine (H). 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