11-60194013-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 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+7842G>T		intron_variant	Intron 2 of 7			ENSP00000497952.2
MS4A4A	ENST00000679553.1	c.59+7842G>T		intron_variant	Intron 1 of 6			ENSP00000505712.1
MS4A4A	ENST00000681288.1	c.59+7842G>T		intron_variant	Intron 2 of 7			ENSP00000505714.1

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

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.360

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11230180; hg19: chr11-59961486;