rs2123314

Variant names:

• chr11-60198822-T-C
• rs2123314
• ENST00000649552.2:c.59+12651T>C

Variant summary

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

The ENST00000649552.2(MS4A4A):​c.59+12651T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,998 control chromosomes in the GnomAD database, including 9,264 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 0.34 (9264 hom., cov: 32)
• Consequence: MS4A4A ENST00000649552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

MS4A4A (HGNC:13371): (membrane spanning 4-domains A4A) This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features, similar intron/exon splice boundaries, and display unique expression patterns in hematopoietic cells and nonlymphoid tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MS4A4A	ENST00000649552.2	c.59+12651T>C		intron_variant	Intron 2 of 7			ENSP00000497952.2
MS4A4A	ENST00000679553.1	c.59+12651T>C		intron_variant	Intron 1 of 6			ENSP00000505712.1
MS4A4A	ENST00000681288.1	c.59+12651T>C		intron_variant	Intron 2 of 7			ENSP00000505714.1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51545 AN: 151878 Hom.: 9260 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.377

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.339 AC: 51583 AN: 151998 Hom.: 9264 Cov.: 32 AF XY: 0.336 AC XY: 24960 AN XY: 74298

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.378

Alfa AF: 0.346 Hom.: 1489

Bravo AF: 0.335

Asia WGS AF: 0.352 AC: 1223 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2123314; hg19: chr11-59966295;