rs655231

chr11-60246384-G-Achr11-60246384-G-T

Variant summary

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

The ENST00000649552.2(MS4A4A):c.60-45841G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,974 control chromosomes in the GnomAD database, including 32,927 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 0.65 (32927 hom., cov: 32)
• Consequence: MS4A4A ENST00000649552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 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.60-45841G>A		intron_variant				A2
MS4A4A	ENST00000679385.1	c.-24-50813G>A		intron_variant
MS4A4A	ENST00000679553.1	c.60-45841G>A		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99071 AN: 151856 Hom.: 32897 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.652 AC: 99159 AN: 151974 Hom.: 32927 Cov.: 32 AF XY: 0.654 AC XY: 48573 AN XY: 74316

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.603

Alfa AF: 0.627 Hom.: 6389

Bravo AF: 0.647

Asia WGS AF: 0.613 AC: 2125 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs655231; hg19: chr11-60013857; COSMIC: COSV69885066;