1-160546518-A-G

Variant names:

• chr1-160546518-A-G
• rs6427528
• NM_003874.4:c.*1738T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 35 publications found

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]

ENSG00000234425 (HGNC:58385):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003874.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD84	NM_003874.4	MANE Select	c.*1738T>C		3_prime_UTR	Exon 7 of 7	NP_003865.1
	CD84	NM_001184879.2		c.*1738T>C		3_prime_UTR	Exon 8 of 8	NP_001171808.1
	CD84	NM_001330742.2		c.*1738T>C		3_prime_UTR	Exon 8 of 8	NP_001317671.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD84	ENST00000368054.8	TSL:1 MANE Select	c.*1738T>C		3_prime_UTR	Exon 7 of 7	ENSP00000357033.4
	CD84	ENST00000534968.5	TSL:1	c.*1738T>C		3_prime_UTR	Exon 6 of 6	ENSP00000442845.1
	ENSG00000234425	ENST00000446952.2	TSL:3	n.144+9331A>G		intron	N/A

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 1.00 AC: 8 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.903 AC: 65 AN: 72

Other (OTH) AF: 1.00 AC: 6 AN: 6

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

African (AFR) AF: 0.588 AC: 24345 AN: 41408

American (AMR) AF: 0.744 AC: 11376 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3016 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4544 AN: 5178

South Asian (SAS) AF: 0.720 AC: 3478 AN: 4830

European-Finnish (FIN) AF: 0.917 AC: 9706 AN: 10584

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61828 AN: 68012

Other (OTH) AF: 0.800 AC: 1687 AN: 2110

Alfa AF: 0.868 Hom.: 210298

Bravo AF: 0.777

Asia WGS AF: 0.778 AC: 2709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.59
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6427528; hg19: chr1-160516308;