NM_015274.3:c.160G>C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_015274.3(MAN2B2):ā€‹c.160G>Cā€‹(p.Ala54Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000475 in 1,613,204 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.00043 ( 1 hom., cov: 33)
Exomes š‘“: 0.00048 ( 8 hom. )

Consequence

MAN2B2
NM_015274.3 missense

Scores

1
3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.85
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 Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.014566481).
BS2
High Homozygotes in GnomAdExome4 at 8 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAN2B2NM_015274.3 linkc.160G>C p.Ala54Pro missense_variant Exon 2 of 19 ENST00000285599.8 NP_056089.1 Q9Y2E5-1
MAN2B2NM_001292038.2 linkc.160G>C p.Ala54Pro missense_variant Exon 2 of 19 NP_001278967.1 Q9Y2E5E9PCD7B7Z754

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAN2B2ENST00000285599.8 linkc.160G>C p.Ala54Pro missense_variant Exon 2 of 19 1 NM_015274.3 ENSP00000285599.3 Q9Y2E5-1
MAN2B2ENST00000504248.5 linkc.160G>C p.Ala54Pro missense_variant Exon 2 of 19 2 ENSP00000423129.1 E9PCD7
MAN2B2ENST00000505907.1 linkc.154G>C p.Ala52Pro missense_variant Exon 2 of 17 2 ENSP00000426273.1 H0YA68

Frequencies

GnomAD3 genomes
AF:
0.000434
AC:
66
AN:
152216
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.0164
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000868
AC:
218
AN:
251060
Hom.:
2
AF XY:
0.000839
AC XY:
114
AN XY:
135842
show subpopulations
Gnomad AFR exome
AF:
0.0000616
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.0177
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000282
Gnomad OTH exome
AF:
0.00114
GnomAD4 exome
AF:
0.000479
AC:
700
AN:
1460988
Hom.:
8
Cov.:
31
AF XY:
0.000472
AC XY:
343
AN XY:
726808
show subpopulations
Gnomad4 AFR exome
AF:
0.0000896
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0180
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000120
Gnomad4 OTH exome
AF:
0.00149
GnomAD4 genome
AF:
0.000434
AC:
66
AN:
152216
Hom.:
1
Cov.:
33
AF XY:
0.000403
AC XY:
30
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.0164
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000761
Hom.:
0
Bravo
AF:
0.000544
ExAC
AF:
0.000634
AC:
77
EpiCase
AF:
0.000327
EpiControl
AF:
0.000533

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.62
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.18
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Benign
0.37
T;.
Eigen
Benign
-0.20
Eigen_PC
Benign
-0.20
FATHMM_MKL
Benign
0.67
D
LIST_S2
Benign
0.82
T;T
M_CAP
Benign
0.0035
T
MetaRNN
Benign
0.015
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.8
L;.
PrimateAI
Uncertain
0.64
T
PROVEAN
Uncertain
-3.2
D;D
REVEL
Benign
0.18
Sift
Benign
0.080
T;T
Sift4G
Benign
0.066
T;T
Polyphen
0.50
P;P
Vest4
0.67
MutPred
0.67
Gain of glycosylation at Y57 (P = 0.0242);Gain of glycosylation at Y57 (P = 0.0242);
MVP
0.29
MPC
0.35
ClinPred
0.094
T
GERP RS
3.0
Varity_R
0.85
gMVP
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs145563570; hg19: chr4-6578326; API