4-6575334-G-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015274.3(MAN2B2):c.124G>T(p.Val42Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000379 in 1,582,288 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
MAN2B2
NM_015274.3 missense
NM_015274.3 missense
Scores
1
11
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.86
Genes affected
MAN2B2 (HGNC:29623): (mannosidase alpha class 2B member 2) Predicted to enable alpha-mannosidase activity. Predicted to be involved in mannose metabolic process. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN2B2 | ENST00000285599.8 | c.124G>T | p.Val42Phe | missense_variant | Exon 1 of 19 | 1 | NM_015274.3 | ENSP00000285599.3 | ||
MAN2B2 | ENST00000504248.5 | c.124G>T | p.Val42Phe | missense_variant | Exon 1 of 19 | 2 | ENSP00000423129.1 | |||
MAN2B2 | ENST00000505907.1 | c.118G>T | p.Val40Phe | missense_variant | Exon 1 of 17 | 2 | ENSP00000426273.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152228Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000995 AC: 2AN: 200910Hom.: 0 AF XY: 0.0000181 AC XY: 2AN XY: 110644
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GnomAD4 exome AF: 0.00000210 AC: 3AN: 1429942Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 709926
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74494
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;N
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MutPred
Gain of glycosylation at Y43 (P = 0.0106);Gain of glycosylation at Y43 (P = 0.0106);
MVP
MPC
ClinPred
D
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Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at