dbSNP rs6427528: CD84:c.*1738T>C (chr1-160546518-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.193

Publications

36 publications found

Variant links:

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]

CD84 links:

ENSG00000234425 (HGNC:58385):

ENSG00000234425 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD84	NM_003874.4	MANE Select	c.*1738T>C	3_prime_UTR	Exon 7 of 7	NP_003865.1	Q9UIB8-3
CD84	NM_001184879.2		c.*1738T>C	3_prime_UTR	Exon 8 of 8	NP_001171808.1	Q9UIB8-1
CD84	NM_001330742.2		c.*1738T>C	3_prime_UTR	Exon 8 of 8	NP_001317671.1	Q9UIB8-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD84	ENST00000368054.8	TSL:1 MANE Select	c.*1738T>C	3_prime_UTR	Exon 7 of 7	ENSP00000357033.4	Q9UIB8-3
CD84	ENST00000534968.5	TSL:1	c.*1738T>C	3_prime_UTR	Exon 6 of 6	ENSP00000442845.1	Q9UIB8-7
CD84	ENST00000898394.1		c.*1738T>C	3_prime_UTR	Exon 7 of 7	ENSP00000568453.1

Frequencies

GnomAD3 genomes

AF:

0.796

AC:

121028

AN:

151982

Hom.:

49605

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.897

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.903

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.796

AC:

121064

AN:

152100

Hom.:

49605

Cov.:

AF XY:

0.793

AC XY:

58997

AN XY:

74364

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1124

2248

3371

4495

5619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

862

1724

2586

3448

4310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.59

PhyloP100

0.19

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over