rs6427528

chr1-160546518-A-G

Variant summary

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

The NM_003874.4(CD84):c.*1738T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,198 control chromosomes in the GnomAD database, including 49,644 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 0.80 (49605 hom., cov: 31)
  • Exomes 𝑓: 0.89 (39 hom.)
• Consequence: CD84 NM_003874.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

CD84 (HGNC:1704): (CD84 molecule) This gene encodes a membrane glycoprotein that is a member of the signaling lymphocyte activation molecule (SLAM) family. This family forms a subset of the larger CD2 cell-surface receptor Ig superfamily. The encoded protein is a homophilic adhesion molecule that is expressed in numerous immune cells types and is involved in regulating receptor-mediated signaling in those cells. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD84	NM_003874.4	c.*1738T>C		3_prime_UTR_variant	7/7	ENST00000368054.8
LOC105371468	XR_922203.3	n.119+9331A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD84	ENST00000368054.8	c.*1738T>C		3_prime_UTR_variant	7/7	1	NM_003874.4
CD84	ENST00000534968.5	c.*1738T>C		3_prime_UTR_variant	6/6	1
	ENST00000446952.1	n.115+9331A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121028 AN: 151982 Hom.: 49605 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.797

GnomAD4 exome AF: 0.888 AC: 87 AN: 98 Hom.: 39 Cov.: 0 AF XY: 0.897 AC XY: 70 AN XY: 78

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.903

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.796 AC: 121064 AN: 152100 Hom.: 49605 Cov.: 31 AF XY: 0.793 AC XY: 58997 AN XY: 74364

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.800

Alfa AF: 0.886 Hom.: 91314

Bravo AF: 0.777

Asia WGS AF: 0.778 AC: 2709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.5
Dann	Benign	0.59

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: rs6427528; hg19: chr1-160516308;