Variant chr11-60069624-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006138.5(MS4A3):c.564C>T(p.Thr188Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,610,468 control chromosomes in the GnomAD database, including 69,586 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 0.27 ( 5848 hom., cov: 32)

Exomes 𝑓: 0.29 ( 63738 hom. )

Consequence

MS4A3
NM_006138.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.239

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]

MS4A3 links:

MS4A3 (HGNC:):

MS4A3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MS4A3	NM_006138.5 linkuse as main transcript	c.564C>T	p.Thr188Thr	synonymous_variant	6/7	ENST00000278865.8	NP_006129.4	Q96HJ5-1
MS4A3	NM_001031809.2 linkuse as main transcript	c.426C>T	p.Thr142Thr	synonymous_variant	5/6		NP_001026979.1	Q96HJ5-2
MS4A3	NM_001031666.2 linkuse as main transcript	c.195C>T	p.Thr65Thr	synonymous_variant	4/5		NP_001026836.1	Q96HJ5-3
MS4A3	XM_011545363.4 linkuse as main transcript	c.384C>T	p.Thr128Thr	synonymous_variant	5/6		XP_011543665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MS4A3	ENST00000278865.8 linkuse as main transcript	c.564C>T	p.Thr188Thr	synonymous_variant	6/7	1	NM_006138.5	ENSP00000278865.3		Q96HJ5-1

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41379

AN:

151890

Hom.:

5847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.229

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.288

GnomAD3 exomes

AF:

0.281

AC:

70477

AN:

250936

Hom.:

11046

AF XY:

0.297

AC XY:

40219

AN XY:

135600

show subpopulations

Gnomad AFR exome

AF:

0.262

Gnomad AMR exome

AF:

0.169

Gnomad ASJ exome

AF:

0.270

Gnomad EAS exome

AF:

0.214

Gnomad SAS exome

AF:

0.486

Gnomad FIN exome

AF:

0.214

Gnomad NFE exome

AF:

0.287

Gnomad OTH exome

AF:

0.272

GnomAD4 exome

AF:

0.288

AC:

419586

AN:

1458460

Hom.:

63738

Cov.:

AF XY:

0.295

AC XY:

213919

AN XY:

725596

show subpopulations

Gnomad4 AFR exome

AF:

0.262

Gnomad4 AMR exome

AF:

0.177

Gnomad4 ASJ exome

AF:

0.276

Gnomad4 EAS exome

AF:

0.189

Gnomad4 SAS exome

AF:

0.487

Gnomad4 FIN exome

AF:

0.215

Gnomad4 NFE exome

AF:

0.284

Gnomad4 OTH exome

AF:

0.291

GnomAD4 genome

AF:

0.272

AC:

41407

AN:

152008

Hom.:

5848

Cov.:

AF XY:

0.273

AC XY:

20318

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.268

Gnomad4 AMR

AF:

0.229

Gnomad4 ASJ

AF:

0.256

Gnomad4 EAS

AF:

0.220

Gnomad4 SAS

AF:

0.489

Gnomad4 FIN

AF:

0.202

Gnomad4 NFE

AF:

0.285

Gnomad4 OTH

AF:

0.292

Alfa

AF:

0.286

Hom.:

15057

Bravo

AF:

0.269

Asia WGS

AF:

0.352

AC:

1224

AN:

3478

EpiCase

AF:

0.301

EpiControl

AF:

0.300

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.53

DANN

Benign

0.47

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.21

Details are displayed if max score is > 0.2

DS_AL_spliceai

0.21

Position offset: -50

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over