11-60266956-C-T

Position:

• chr11-60266956-C-T

Variant summary

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

The ENST00000649552.2(MS4A4A):​c.60-25269C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 151,862 control chromosomes in the GnomAD database, including 30,468 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 (30468 hom., cov: 30)
• Consequence: MS4A4A ENST00000649552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60266956C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MS4A4A	ENST00000649552.2	c.60-25269C>T		intron_variant				ENSP00000497952.2
MS4A4A	ENST00000679553.1	c.60-25269C>T		intron_variant				ENSP00000505712.1
MS4A4A	ENST00000681288.1	c.60-25269C>T		intron_variant				ENSP00000505714.1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95684 AN: 151744 Hom.: 30456 Cov.: 30

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.630 AC: 95738 AN: 151862 Hom.: 30468 Cov.: 30 AF XY: 0.634 AC XY: 47036 AN XY: 74220

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.591

Alfa AF: 0.596 Hom.: 46634

Bravo AF: 0.622

Asia WGS AF: 0.621 AC: 2159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4938933; hg19: chr11-60034429;