chr11-60198822-T-C

Position:

• chr11-60198822-T-C

Variant summary

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

The ENST00000649552.2(MS4A4A):​c.59+12651T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,998 control chromosomes in the GnomAD database, including 9,264 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 0.34 (9264 hom., cov: 32)
• Consequence: MS4A4A ENST00000649552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60198822T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MS4A4A	ENST00000649552.2	c.59+12651T>C		intron_variant				ENSP00000497952.2
MS4A4A	ENST00000679553.1	c.59+12651T>C		intron_variant				ENSP00000505712.1
MS4A4A	ENST00000681288.1	c.59+12651T>C		intron_variant				ENSP00000505714.1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51545 AN: 151878 Hom.: 9260 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.339 AC: 51583 AN: 151998 Hom.: 9264 Cov.: 32 AF XY: 0.336 AC XY: 24960 AN XY: 74298

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.378

Alfa AF: 0.346 Hom.: 1489

Bravo AF: 0.335

Asia WGS AF: 0.352 AC: 1223 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2123314; hg19: chr11-59966295;