rs10792258

Positions:

• chr11-60254847-C-T

Variant summary

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

The ENST00000649552.2(MS4A4A):​c.60-37378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,206 control chromosomes in the GnomAD database, including 4,845 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 0.24 (4845 hom., cov: 32)
• Consequence: MS4A4A ENST00000649552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MS4A4A	ENST00000649552.2	c.60-37378C>T		intron_variant				ENSP00000497952	A2
MS4A4A	ENST00000679385.1	c.-24-42350C>T		intron_variant				ENSP00000506313
MS4A4A	ENST00000679553.1	c.60-37378C>T		intron_variant				ENSP00000505712	A2

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35923 AN: 152088 Hom.: 4844 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.236 AC: 35941 AN: 152206 Hom.: 4845 Cov.: 32 AF XY: 0.232 AC XY: 17269 AN XY: 74410

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.226

Alfa AF: 0.222 Hom.: 501

Bravo AF: 0.246

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10792258; hg19: chr11-60022320;