dbSNP rs1285933: MGAM:c.-179-18472G>A (chr7-141927349-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000465654.5(MGAM):c.-179-18472G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,056 control chromosomes in the GnomAD database, including 21,650 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 0.53 ( 21648 hom., cov: 32)

Exomes 𝑓: 0.43 ( 2 hom. )

Consequence

MGAM
ENST00000465654.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260

Publications

32 publications found

Variant links:

COSMIC-nc: COSV107521610

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]

MGAM links:

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]

CLEC5A links:

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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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CLEC5A	NM_013252.3 link	c.*2755C>T	downstream_gene_variant	ENST00000546910.6	NP_037384.1	Q9NY25-1A4D1U7
CLEC5A	NM_001301167.2 link	c.*2755C>T	downstream_gene_variant		NP_001288096.1	Q14DL9
CLEC5A	XM_011515995.3 link	c.*2755C>T	downstream_gene_variant		XP_011514297.1
CLEC5A	XR_007059995.1 link	n.*8C>T	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MGAM	ENST00000465654.5 link	c.-179-18472G>A	intron_variant	Intron 1 of 5	3		ENSP00000419372.1	E7EW87
MGAM	ENST00000497554.1 link	n.37-2428G>A	intron_variant	Intron 1 of 2	3
CLEC5A	ENST00000546910.6 link	c.*2755C>T	downstream_gene_variant		1	NM_013252.3	ENSP00000449999.1	Q9NY25-1

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80396

AN:

151924

Hom.:

21637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.746

Gnomad AMR

AF:

0.465

Gnomad ASJ

AF:

0.551

Gnomad EAS

AF:

0.216

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.521

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.522

Gnomad OTH

AF:

0.519

GnomAD4 exome

AF:

0.429

AC:

AN:

Hom.:

Cov.:

AF XY:

0.429

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.167

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.529

AC:

80439

AN:

152042

Hom.:

21648

Cov.:

AF XY:

0.523

AC XY:

38877

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.612

AC:

25392

AN:

41466

American (AMR)

AF:

0.465

AC:

7107

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.551

AC:

1910

AN:

3468

East Asian (EAS)

AF:

0.217

AC:

1121

AN:

5162

South Asian (SAS)

AF:

0.416

AC:

2007

AN:

4822

European-Finnish (FIN)

AF:

0.521

AC:

5502

AN:

10562

Middle Eastern (MID)

AF:

0.507

AC:

149

AN:

294

European-Non Finnish (NFE)

AF:

0.522

AC:

35487

AN:

67960

Other (OTH)

AF:

0.514

AC:

1085

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1920

3841

5761

7682

9602

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.523

Hom.:

35561

Bravo

AF:

0.525

Asia WGS

AF:

0.315

AC:

1096

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.82

(source)

DANN

Benign

0.65

PhyloP100

-0.026

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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rs1285933

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over