11-60171834-T-G

Variant names:

• chr11-60171834-T-G
• rs610932
• NM_152852.3:c.*324A>C

Variant summary

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

The NM_152852.3(MS4A6A):​c.*324A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,962 control chromosomes in the GnomAD database, including 25,145 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 0.57 (25145 hom., cov: 31)
• Consequence: MS4A6A NM_152852.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

MS4A6A (HGNC:13375): (membrane spanning 4-domains A6A) 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 11q12.1, among a cluster of family members. Alternative splicing of this gene results in several transcript variants that encode different protein isoforms. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MS4A6A	NM_152852.3	c.*324A>C		3_prime_UTR_variant	Exon 8 of 8		NP_690591.1
MS4A6A	NM_152851.2	c.*430A>C		3_prime_UTR_variant	Exon 7 of 7		NP_690590.1
MS4A6A	XM_005274177.4	c.*324A>C		3_prime_UTR_variant	Exon 8 of 8		XP_005274234.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MS4A6A	ENST00000420732.6	c.*430A>C		downstream_gene_variant		1		ENSP00000392921.2
MS4A6A	ENST00000529054.5	c.*324A>C		downstream_gene_variant		5		ENSP00000435844.1
MS4A6A	ENST00000530839.5	c.*324A>C		downstream_gene_variant		2		ENSP00000436979.1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86888 AN: 151846 Hom.: 25134 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.572 AC: 86929 AN: 151962 Hom.: 25145 Cov.: 31 AF XY: 0.577 AC XY: 42861 AN XY: 74298

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.545

Alfa AF: 0.569 Hom.: 54282

Bravo AF: 0.568

Asia WGS AF: 0.527 AC: 1830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs610932; hg19: chr11-59939307; COSMIC: COSV60616357;