Variant 11-60463058-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_152866.3(MS4A1):c.216C>T(p.Ile72Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0784 in 1,614,060 control chromosomes in the GnomAD database, including 5,805 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 323 hom., cov: 32)

Exomes 𝑓: 0.081 ( 5482 hom. )

Consequence

MS4A1
NM_152866.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.427

Variant links:

Genes affected

MS4A1 (HGNC:7315): (membrane spanning 4-domains A1) This gene encodes 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 gene encodes a B-lymphocyte surface molecule which plays a role in the development and differentiation of B-cells into plasma cells. This family member is localized to 11q12, among a cluster of family members. Alternative splicing of this gene results in two transcript variants which encode the same protein. [provided by RefSeq, Jul 2008]

MS4A1 links:

MS4A1 (HGNC:):

MS4A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 11-60463058-C-T is Benign according to our data. Variant chr11-60463058-C-T is described in ClinVar as [Benign]. Clinvar id is 618716.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.427 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MS4A1	NM_152866.3 linkuse as main transcript	c.216C>T	p.Ile72Ile	synonymous_variant	4/8	ENST00000345732.9	NP_690605.1	P11836-1A0A024R507
MS4A1	NM_021950.4 linkuse as main transcript	c.216C>T	p.Ile72Ile	synonymous_variant	3/7		NP_068769.2	P11836-1A0A024R507
MS4A1	NM_152867.2 linkuse as main transcript	c.216C>T	p.Ile72Ile	synonymous_variant	3/7		NP_690606.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MS4A1	ENST00000345732.9 linkuse as main transcript	c.216C>T	p.Ile72Ile	synonymous_variant	4/8	1	NM_152866.3	ENSP00000314620.7		P11836-1

Frequencies

GnomAD3 genomes

AF:

0.0565

AC:

8598

AN:

152116

Hom.:

323

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0199

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.0386

Gnomad ASJ

AF:

0.0441

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.0315

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0758

Gnomad OTH

AF:

0.0499

GnomAD3 exomes

AF:

0.0714

AC:

17942

AN:

251282

Hom.:

890

AF XY:

0.0780

AC XY:

10595

AN XY:

135810

show subpopulations

Gnomad AFR exome

AF:

0.0189

Gnomad AMR exome

AF:

0.0277

Gnomad ASJ exome

AF:

0.0402

Gnomad EAS exome

AF:

0.0950

Gnomad SAS exome

AF:

0.158

Gnomad FIN exome

AF:

0.0345

Gnomad NFE exome

AF:

0.0757

Gnomad OTH exome

AF:

0.0549

GnomAD4 exome

AF:

0.0807

AC:

117930

AN:

1461826

Hom.:

5482

Cov.:

AF XY:

0.0834

AC XY:

60622

AN XY:

727206

show subpopulations

Gnomad4 AFR exome

AF:

0.0184

Gnomad4 AMR exome

AF:

0.0287

Gnomad4 ASJ exome

AF:

0.0412

Gnomad4 EAS exome

AF:

0.127

Gnomad4 SAS exome

AF:

0.158

Gnomad4 FIN exome

AF:

0.0365

Gnomad4 NFE exome

AF:

0.0807

Gnomad4 OTH exome

AF:

0.0696

GnomAD4 genome

AF:

0.0565

AC:

8596

AN:

152234

Hom.:

323

Cov.:

AF XY:

0.0566

AC XY:

4212

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0199

Gnomad4 AMR

AF:

0.0385

Gnomad4 ASJ

AF:

0.0441

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.166

Gnomad4 FIN

AF:

0.0315

Gnomad4 NFE

AF:

0.0758

Gnomad4 OTH

AF:

0.0493

Alfa

AF:

0.0726

Hom.:

394

Bravo

AF:

0.0524

Asia WGS

AF:

0.130

AC:

453

AN:

3478

EpiCase

AF:

0.0766

EpiControl

AF:

0.0775

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Immunodeficiency, common variable, 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Nov 29, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

8.0

DANN

Benign

0.69

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over