rs1373061

Variant names:

• chr11-60358174-A-C
• rs1373061
• ENST00000532756.1:n.*162+17246A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-60358174-A-C
• chr11-60358174-A-G
• chr11-60358174-A-T

Variant summary

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

The ENST00000532756.1(MS4A6E):​n.*162+17246A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,240 control chromosomes in the GnomAD database, including 65,198 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 0.92 (65198 hom., cov: 32)
• Consequence: MS4A6E ENST00000532756.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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
MS4A6E	ENST00000532756.1	n.*162+17246A>C		intron_variant	Intron 4 of 4	4		ENSP00000432963.1

Frequencies

GnomAD3 genomes AF: 0.920 AC: 140015 AN: 152122 Hom.: 65167 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.965

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.920 AC: 140100 AN: 152240 Hom.: 65198 Cov.: 32 AF XY: 0.919 AC XY: 68430 AN XY: 74438

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.994

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.965

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.933

Alfa AF: 0.971 Hom.: 14307

Bravo AF: 0.907

Asia WGS AF: 0.919 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1373061; hg19: chr11-60125647;