11-60331752-T-C

Variant names:

• chr11-60331752-T-C
• rs4939338
• NM_139249.4:c.-14-3130T>C

Variant summary

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

The NM_139249.4(MS4A6E):​c.-14-3130T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,054 control chromosomes in the GnomAD database, including 30,423 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 0.63 (30423 hom., cov: 32)
• Consequence: MS4A6E NM_139249.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 9 publications found

Genes affected

MS4A6E (HGNC:14285): (membrane spanning 4-domains A6E) This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. The gene encoding this protein is localized to 11q12.3, among a cluster of family members. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MS4A6E	NM_139249.4	c.-14-3130T>C		intron_variant	Intron 1 of 4	ENST00000684409.1	NP_640342.1
MS4A6E	NR_170614.1	n.155-3130T>C		intron_variant	Intron 1 of 5
MS4A6E	NR_170615.1	n.155-3130T>C		intron_variant	Intron 1 of 4
MS4A6E	NR_170616.1	n.155-3130T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MS4A6E	ENST00000684409.1	c.-14-3130T>C		intron_variant	Intron 1 of 4		NM_139249.4	ENSP00000507799.1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95827 AN: 151936 Hom.: 30384 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.631 AC: 95928 AN: 152054 Hom.: 30423 Cov.: 32 AF XY: 0.635 AC XY: 47182 AN XY: 74340

African (AFR) AF: 0.613 AC: 25393 AN: 41412

American (AMR) AF: 0.613 AC: 9372 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2240 AN: 3468

East Asian (EAS) AF: 0.675 AC: 3501 AN: 5188

South Asian (SAS) AF: 0.495 AC: 2386 AN: 4818

European-Finnish (FIN) AF: 0.784 AC: 8311 AN: 10596

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42631 AN: 67978

Other (OTH) AF: 0.611 AC: 1288 AN: 2108

Alfa AF: 0.643 Hom.: 4086

Bravo AF: 0.618

Asia WGS AF: 0.594 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs4939338; hg19: chr11-60099225;