rs1562990

chr11-60255614-C-Achr11-60255614-C-T

Variant summary

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

The ENST00000649552.2(MS4A4A):c.60-36611C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,106 control chromosomes in the GnomAD database, including 34,463 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 0.66 (34463 hom., cov: 32)
• Consequence: MS4A4A ENST00000649552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

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 (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MS4A4A	ENST00000649552.2	c.60-36611C>A		intron_variant				A2
MS4A4A	ENST00000679385.1	c.-24-41583C>A		intron_variant
MS4A4A	ENST00000679553.1	c.60-36611C>A		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101007 AN: 151988 Hom.: 34423 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.665 AC: 101104 AN: 152106 Hom.: 34463 Cov.: 32 AF XY: 0.666 AC XY: 49498 AN XY: 74356

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.612

Alfa AF: 0.591 Hom.: 38172

Bravo AF: 0.661

Asia WGS AF: 0.617 AC: 2146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.30
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562990; hg19: chr11-60023087;