11-60194013-G-T

Variant names:

• chr11-60194013-G-T
• rs11230180
• ENST00000649552.2:c.59+7842G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649552.2(MS4A4A):​c.59+7842G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,018 control chromosomes in the GnomAD database, including 8,285 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 0.31 (8285 hom., cov: 32)
• Consequence: MS4A4A ENST00000649552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 19 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MS4A4A	ENST00000649552.2		c.59+7842G>T		intron	N/A	ENSP00000497952.2	A0A3B3ITV6
	MS4A4A	ENST00000679553.1		c.59+7842G>T		intron	N/A	ENSP00000505712.1	A0A7P0T9I4
	MS4A4A	ENST00000681288.1		c.59+7842G>T		intron	N/A	ENSP00000505714.1	A0A7P0T9I4

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46756 AN: 151900 Hom.: 8285 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.308 AC: 46768 AN: 152018 Hom.: 8285 Cov.: 32 AF XY: 0.306 AC XY: 22742 AN XY: 74296

African (AFR) AF: 0.143 AC: 5949 AN: 41488

American (AMR) AF: 0.292 AC: 4454 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1327 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1127 AN: 5174

South Asian (SAS) AF: 0.493 AC: 2372 AN: 4812

European-Finnish (FIN) AF: 0.277 AC: 2921 AN: 10554

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27329 AN: 67926

Other (OTH) AF: 0.360 AC: 762 AN: 2116

Alfa AF: 0.346 Hom.: 1325

Bravo AF: 0.299

Asia WGS AF: 0.342 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.22
PhyloP100		0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11230180;

hg19: chr11-59961486;