4-6575334-G-T

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

Scores

1
11
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.86
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAN2B2NM_015274.3 linkc.124G>T p.Val42Phe missense_variant Exon 1 of 19 ENST00000285599.8 NP_056089.1 Q9Y2E5-1
MAN2B2NM_001292038.2 linkc.124G>T p.Val42Phe missense_variant Exon 1 of 19 NP_001278967.1 Q9Y2E5E9PCD7B7Z754

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAN2B2ENST00000285599.8 linkc.124G>T p.Val42Phe missense_variant Exon 1 of 19 1 NM_015274.3 ENSP00000285599.3 Q9Y2E5-1
MAN2B2ENST00000504248.5 linkc.124G>T p.Val42Phe missense_variant Exon 1 of 19 2 ENSP00000423129.1 E9PCD7
MAN2B2ENST00000505907.1 linkc.118G>T p.Val40Phe missense_variant Exon 1 of 17 2 ENSP00000426273.1 H0YA68

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152228
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000995
AC:
2
AN:
200910
Hom.:
0
AF XY:
0.0000181
AC XY:
2
AN XY:
110644
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000753
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000210
AC:
3
AN:
1429942
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
709926
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000363
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000197
AC:
3
AN:
152346
Hom.:
0
Cov.:
33
AF XY:
0.0000403
AC XY:
3
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.0000167
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.63
BayesDel_addAF
Benign
-0.0095
T
BayesDel_noAF
Uncertain
-0.060
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.22
T;.
Eigen
Uncertain
0.26
Eigen_PC
Benign
0.12
FATHMM_MKL
Benign
0.72
D
LIST_S2
Uncertain
0.91
D;D
M_CAP
Benign
0.035
D
MetaRNN
Uncertain
0.50
D;D
MetaSVM
Benign
-0.30
T
MutationAssessor
Uncertain
2.6
M;.
PrimateAI
Uncertain
0.68
T
PROVEAN
Uncertain
-2.4
N;N
REVEL
Uncertain
0.57
Sift
Uncertain
0.010
D;D
Sift4G
Uncertain
0.0060
D;D
Polyphen
0.99
D;D
Vest4
0.64
MutPred
0.77
Gain of glycosylation at Y43 (P = 0.0106);Gain of glycosylation at Y43 (P = 0.0106);
MVP
0.71
MPC
0.61
ClinPred
0.95
D
GERP RS
0.63
Varity_R
0.76
gMVP
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs376407727; hg19: chr4-6577061; API