ENST00000649552.2:c.60-40548C>T

Variant names:

• chr11-60251677-C-T
• rs636317
• ENST00000649552.2:c.60-40548C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649552.2(MS4A4A):​c.60-40548C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 152,034 control chromosomes in the GnomAD database, including 31,034 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 0.64 (31034 hom., cov: 31)
• Consequence: MS4A4A ENST00000649552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 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.60-40548C>T		intron_variant	Intron 2 of 7			ENSP00000497952.2
MS4A4A	ENST00000679553.1	c.60-40548C>T		intron_variant	Intron 1 of 6			ENSP00000505712.1
MS4A4A	ENST00000681288.1	c.60-40548C>T		intron_variant	Intron 2 of 7			ENSP00000505714.1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96556 AN: 151916 Hom.: 31020 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.635 AC: 96614 AN: 152034 Hom.: 31034 Cov.: 31 AF XY: 0.638 AC XY: 47441 AN XY: 74304

African (AFR) AF: 0.711 AC: 29448 AN: 41436

American (AMR) AF: 0.588 AC: 8983 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2125 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3491 AN: 5152

South Asian (SAS) AF: 0.497 AC: 2393 AN: 4812

European-Finnish (FIN) AF: 0.733 AC: 7738 AN: 10562

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40433 AN: 68010

Other (OTH) AF: 0.594 AC: 1252 AN: 2106

Alfa AF: 0.633 Hom.: 3968

Bravo AF: 0.627

Asia WGS AF: 0.610 AC: 2122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	17
DANN	Benign	0.89
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs636317; hg19: chr11-60019150;