chr1-160712046-C-T

Variant names:

• chr1-160712046-C-T
• rs352685
• NM_001778.4:c.-283G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001778.4(CD48):​c.-283G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: CD48 NM_001778.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 7 publications found

Genes affected

CD48 (HGNC:1683): (CD48 molecule) This gene encodes a member of the CD2 subfamily of immunoglobulin-like receptors which includes SLAM (signaling lymphocyte activation molecules) proteins. The encoded protein is found on the surface of lymphocytes and other immune cells, dendritic cells and endothelial cells, and participates in activation and differentiation pathways in these cells. The encoded protein does not have a transmembrane domain, however, but is held at the cell surface by a GPI anchor via a C-terminal domain which maybe cleaved to yield a soluble form of the receptor. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD48	NM_001778.4	c.-283G>A		upstream_gene_variant		ENST00000368046.8	NP_001769.2
CD48	NM_001256030.2	c.-283G>A		upstream_gene_variant			NP_001242959.1
CD48	XM_005245625.1	c.-283G>A		upstream_gene_variant			XP_005245682.1
CD48	XM_017002867.3	c.-283G>A		upstream_gene_variant			XP_016858356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD48	ENST00000368046.8	c.-283G>A		upstream_gene_variant		1	NM_001778.4	ENSP00000357025.3
CD48	ENST00000613788.1	c.-283G>A		upstream_gene_variant		1		ENSP00000484431.1
CD48	ENST00000368045.3	c.-283G>A		upstream_gene_variant		1		ENSP00000357024.3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.65
PhyloP100		1.2
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs352685; hg19: chr1-160681836;