rs2868121

Variant names:

• chr11-60332956-G-A
• rs2868121
• NM_139249.4:c.-14-1926G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-60332956-G-A
• chr11-60332956-G-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.-14-1926G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,080 control chromosomes in the GnomAD database, including 10,274 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 0.36 (10274 hom., cov: 33)
• Consequence: MS4A6E NM_139249.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MS4A6E	NM_139249.4	c.-14-1926G>A		intron_variant	Intron 1 of 4	ENST00000684409.1	NP_640342.1
MS4A6E	NR_170614.1	n.155-1926G>A		intron_variant	Intron 1 of 5
MS4A6E	NR_170615.1	n.155-1926G>A		intron_variant	Intron 1 of 4
MS4A6E	NR_170616.1	n.155-1926G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MS4A6E	ENST00000684409.1	c.-14-1926G>A		intron_variant	Intron 1 of 4		NM_139249.4	ENSP00000507799.1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54387 AN: 151962 Hom.: 10252 Cov.: 33

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.358 AC: 54453 AN: 152080 Hom.: 10274 Cov.: 33 AF XY: 0.366 AC XY: 27223 AN XY: 74316

African (AFR) AF: 0.307 AC: 12753 AN: 41490

American (AMR) AF: 0.396 AC: 6058 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2113 AN: 5174

South Asian (SAS) AF: 0.193 AC: 928 AN: 4818

European-Finnish (FIN) AF: 0.583 AC: 6147 AN: 10544

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24380 AN: 67988

Other (OTH) AF: 0.338 AC: 711 AN: 2106

Alfa AF: 0.351 Hom.: 1581

Bravo AF: 0.345

Asia WGS AF: 0.293 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.62
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2868121; hg19: chr11-60100429;