11-60246384-G-A

Variant names:

• chr11-60246384-G-A
• rs655231
• ENST00000649552.2:c.60-45841G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649552.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MS4A4A	ENST00000649552.2		c.60-45841G>A		intron	N/A	ENSP00000497952.2
	MS4A4A	ENST00000679553.1		c.60-45841G>A		intron	N/A	ENSP00000505712.1
	MS4A4A	ENST00000681288.1		c.60-45841G>A		intron	N/A	ENSP00000505714.1

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

African (AFR) AF: 0.770 AC: 31942 AN: 41468

American (AMR) AF: 0.594 AC: 9064 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2125 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3506 AN: 5180

South Asian (SAS) AF: 0.493 AC: 2377 AN: 4822

European-Finnish (FIN) AF: 0.732 AC: 7716 AN: 10542

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40403 AN: 67910

Other (OTH) AF: 0.603 AC: 1273 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.18
PhyloP100		0.025

Splicing

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

Other links and lift over

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