rs1562990

Variant names:

• chr11-60255614-C-A
• rs1562990
• ENST00000649552.2:c.60-36611C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-60255614-C-A
• chr11-60255614-C-T

Variant summary

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

The ENST00000649552.2(MS4A4A):​c.60-36611C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,106 control chromosomes in the GnomAD database, including 34,463 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 0.66 (34463 hom., cov: 32)
• Consequence: MS4A4A ENST00000649552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

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]

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 (AFR) allele frequency at 95% confidence interval = 0.811 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
MS4A4A	ENST00000649552.2	c.60-36611C>A		intron_variant	Intron 2 of 7			ENSP00000497952.2
MS4A4A	ENST00000679553.1	c.60-36611C>A		intron_variant	Intron 1 of 6			ENSP00000505712.1
MS4A4A	ENST00000681288.1	c.60-36611C>A		intron_variant	Intron 2 of 7			ENSP00000505714.1

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101007 AN: 151988 Hom.: 34423 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.665 AC: 101104 AN: 152106 Hom.: 34463 Cov.: 32 AF XY: 0.666 AC XY: 49498 AN XY: 74356

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.612

Alfa AF: 0.591 Hom.: 38172

Bravo AF: 0.661

Asia WGS AF: 0.617 AC: 2146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562990; hg19: chr11-60023087;