chr11-60070226-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_006138.5(MS4A3):​c.638C>T​(p.Ser213Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000005 in 1,599,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000067 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

MS4A3
NM_006138.5 missense

Scores

1
3
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.40
Variant links:
Genes affected
MS4A3 (HGNC:7317): (membrane spanning 4-domains A3) This gene encodes a member of the membrane-spanning 4A gene family. Members of this 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 likely plays a role in signal transduction and may function as a subunit associated with receptor complexes. The gene encoding this protein is localized to 11q12, among a cluster of related family members. Alternative splicing may result in multiple transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.14883652).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MS4A3NM_006138.5 linkuse as main transcriptc.638C>T p.Ser213Phe missense_variant 7/7 ENST00000278865.8
MS4A3NM_001031809.2 linkuse as main transcriptc.500C>T p.Ser167Phe missense_variant 6/6
MS4A3NM_001031666.2 linkuse as main transcriptc.269C>T p.Ser90Phe missense_variant 5/5
MS4A3XM_011545363.4 linkuse as main transcriptc.458C>T p.Ser153Phe missense_variant 6/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MS4A3ENST00000278865.8 linkuse as main transcriptc.638C>T p.Ser213Phe missense_variant 7/71 NM_006138.5 P1Q96HJ5-1

Frequencies

GnomAD3 genomes
AF:
0.00000671
AC:
1
AN:
149080
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000670
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000125
AC:
3
AN:
239522
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
129418
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000901
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000483
AC:
7
AN:
1450286
Hom.:
0
Cov.:
29
AF XY:
0.00000277
AC XY:
2
AN XY:
722142
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000112
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:
9.07e-7
Gnomad4 OTH exome
AF:
0.0000167
GnomAD4 genome
AF:
0.00000671
AC:
1
AN:
149080
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
72690
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000670
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000189

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsSep 30, 2022The c.638C>T (p.S213F) alteration is located in exon 7 (coding exon 6) of the MS4A3 gene. This alteration results from a C to T substitution at nucleotide position 638, causing the serine (S) at amino acid position 213 to be replaced by a phenylalanine (F). 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
Benign
0.14
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
21
DANN
Uncertain
1.0
DEOGEN2
Benign
0.18
.;.;T;.
Eigen
Benign
0.033
Eigen_PC
Benign
-0.18
FATHMM_MKL
Benign
0.071
N
LIST_S2
Benign
0.53
T;T;.;.
M_CAP
Benign
0.0061
T
MetaRNN
Benign
0.15
T;T;T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
1.9
.;.;L;.
MutationTaster
Benign
1.0
N;N;N;N
PrimateAI
Benign
0.32
T
PROVEAN
Uncertain
-3.4
D;D;D;D
REVEL
Benign
0.043
Sift
Pathogenic
0.0
D;D;D;D
Sift4G
Uncertain
0.0070
D;D;D;D
Polyphen
1.0, 1.0
.;D;D;D
Vest4
0.11
MutPred
0.33
.;.;Gain of catalytic residue at S213 (P = 0.0093);.;
MVP
0.061
MPC
0.082
ClinPred
0.82
D
GERP RS
3.3
Varity_R
0.17
gMVP
0.34

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs1452148190; hg19: chr11-59837699; API