rs3802957

chr11-60469937-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152866.3(MS4A1):c.*1469C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 151,912 control chromosomes in the GnomAD database, including 268 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 0.050 (268 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: MS4A1 NM_152866.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MS4A1	NM_152866.3	c.*1469C>T		3_prime_UTR_variant	8/8	ENST00000345732.9
MS4A1	NM_021950.4	c.*1469C>T		3_prime_UTR_variant	7/7
MS4A1	NM_152867.2	c.*1469C>T		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MS4A1	ENST00000345732.9	c.*1469C>T		3_prime_UTR_variant	8/8	1	NM_152866.3	P1

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 7618 AN: 151794 Hom.: 268 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0520

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0397

Gnomad OTH AF: 0.0495

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0502 AC: 7628 AN: 151912 Hom.: 268 Cov.: 32 AF XY: 0.0533 AC XY: 3955 AN XY: 74254

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.0330

Gnomad4 ASJ AF: 0.0520

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.0397

Gnomad4 OTH AF: 0.0490

Alfa AF: 0.0432 Hom.: 213

Bravo AF: 0.0482

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.7
Dann	Benign	0.27

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

Other links and lift over

dbSNP: rs3802957; hg19: chr11-60237410;