11-60090365-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_000139.5(MS4A2):ā€‹c.216C>Gā€‹(p.Cys72Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

MS4A2
NM_000139.5 missense

Scores

3
5
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.151
Variant links:
Genes affected
MS4A2 (HGNC:7316): (membrane spanning 4-domains A2) The allergic response involves the binding of allergen to receptor-bound IgE followed by cell activation and the release of mediators responsible for the manifestations of allergy. The IgE-receptor, a tetramer composed of an alpha, beta, and 2 disulfide-linked gamma chains, is found on the surface of mast cells and basophils. This gene encodes the beta subunit of the high affinity IgE receptor which is a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. This family member is localized to 11q12, among a cluster of membrane-spanning 4A gene family members. Alternative splicing results in multiple transcript variants encoding distinct proteins. Additional transcript variants have been described but require experimental validation. [provided by RefSeq, Mar 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.805

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MS4A2NM_000139.5 linkc.216C>G p.Cys72Trp missense_variant Exon 3 of 7 ENST00000278888.8 NP_000130.1 Q01362

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MS4A2ENST00000278888.8 linkc.216C>G p.Cys72Trp missense_variant Exon 3 of 7 1 NM_000139.5 ENSP00000278888.3 Q01362
MS4A2ENST00000617306.1 linkc.186+544C>G intron_variant Intron 2 of 5 1 ENSP00000482594.1 A0A0B4J2E9
MS4A2ENST00000440896.2 linkn.318C>G non_coding_transcript_exon_variant Exon 3 of 5 1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461030
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
726858
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Dec 02, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.216C>G (p.C72W) alteration is located in exon 3 (coding exon 3) of the MS4A2 gene. This alteration results from a C to G substitution at nucleotide position 216, causing the cysteine (C) at amino acid position 72 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.82
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.21
T
Eigen
Benign
-0.15
Eigen_PC
Benign
-0.31
FATHMM_MKL
Benign
0.43
N
LIST_S2
Benign
0.52
T
M_CAP
Benign
0.015
T
MetaRNN
Pathogenic
0.80
D
MetaSVM
Benign
-0.98
T
MutationAssessor
Uncertain
2.6
M
PrimateAI
Uncertain
0.56
T
PROVEAN
Pathogenic
-5.3
D
REVEL
Benign
0.22
Sift
Uncertain
0.0080
D
Sift4G
Uncertain
0.017
D
Polyphen
1.0
D
Vest4
0.67
MutPred
0.62
Loss of catalytic residue at M70 (P = 3e-04);
MVP
0.55
MPC
0.18
ClinPred
0.99
D
GERP RS
-1.1
Varity_R
0.87
gMVP
0.41

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-59857838; API