7-141947222-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000465654.5(MGAM):c.-3+1225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,098 control chromosomes in the GnomAD database, including 32,936 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: 𝑓 0.66 ( 32936 hom., cov: 33)
Consequence
MGAM
ENST00000465654.5 intron
ENST00000465654.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.331
Publications
6 publications found
Genes affected
MGAM (HGNC:7043): (maltase-glucoamylase) This gene encodes maltase-glucoamylase, which is a brush border membrane enzyme that plays a role in the final steps of digestion of starch. The protein has two catalytic sites identical to those of sucrase-isomaltase, but the proteins are only 59% homologous. Both are members of glycosyl hydrolase family 31, which has a variety of substrate specificities. [provided by RefSeq, Jul 2008]
CLEC5A (HGNC:2054): (C-type lectin domain containing 5A) This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type II transmembrane protein interacts with dnax-activation protein 12 and may play a role in cell activation. Alternative splice variants have been described but their full-length sequence has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLEC5A | NM_013252.3 | c.-436T>C | upstream_gene_variant | ENST00000546910.6 | NP_037384.1 | |||
CLEC5A | NM_001301167.2 | c.-436T>C | upstream_gene_variant | NP_001288096.1 | ||||
CLEC5A | XM_011515995.3 | c.-436T>C | upstream_gene_variant | XP_011514297.1 | ||||
CLEC5A | XR_007059995.1 | n.-248T>C | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MGAM | ENST00000465654.5 | c.-3+1225A>G | intron_variant | Intron 2 of 5 | 3 | ENSP00000419372.1 | ||||
CLEC5A | ENST00000546910.6 | c.-436T>C | upstream_gene_variant | 1 | NM_013252.3 | ENSP00000449999.1 | ||||
CLEC5A | ENST00000418498.5 | n.-436T>C | upstream_gene_variant | 1 | ENSP00000392561.1 |
Frequencies
GnomAD3 genomes AF: 0.656 AC: 99665AN: 151980Hom.: 32928 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
99665
AN:
151980
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.656 AC: 99709AN: 152098Hom.: 32936 Cov.: 33 AF XY: 0.651 AC XY: 48411AN XY: 74340 show subpopulations
GnomAD4 genome
AF:
AC:
99709
AN:
152098
Hom.:
Cov.:
33
AF XY:
AC XY:
48411
AN XY:
74340
show subpopulations
African (AFR)
AF:
AC:
26567
AN:
41476
American (AMR)
AF:
AC:
9129
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
2337
AN:
3466
East Asian (EAS)
AF:
AC:
2477
AN:
5178
South Asian (SAS)
AF:
AC:
2816
AN:
4822
European-Finnish (FIN)
AF:
AC:
7165
AN:
10582
Middle Eastern (MID)
AF:
AC:
196
AN:
294
European-Non Finnish (NFE)
AF:
AC:
46868
AN:
67998
Other (OTH)
AF:
AC:
1380
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1783
3566
5349
7132
8915
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
798
1596
2394
3192
3990
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1798
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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