rs10489639

chr1-160709737-G-A

Variant summary

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

The NM_001778.4(CD48):c.82+1945C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,012 control chromosomes in the GnomAD database, including 21,559 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 0.52 (21559 hom., cov: 32)
• Consequence: CD48 NM_001778.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD48	NM_001778.4	c.82+1945C>T		intron_variant		ENST00000368046.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD48	ENST00000368046.8	c.82+1945C>T		intron_variant		1	NM_001778.4	P1
CD48	ENST00000368045.3	c.82+1945C>T		intron_variant		1
CD48	ENST00000613788.1	c.82+1945C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79317 AN: 151894 Hom.: 21557 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.522 AC: 79344 AN: 152012 Hom.: 21559 Cov.: 32 AF XY: 0.512 AC XY: 38079 AN XY: 74316

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.535

Alfa AF: 0.594 Hom.: 55927

Bravo AF: 0.522

Asia WGS AF: 0.331 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.3
Dann	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489639; hg19: chr1-160679527;