dbSNP rs3733910: CD180:p.Thr494Thr (chr5-67183361-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005582.3(CD180):c.1482C>T(p.Thr494Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0229 in 1,614,062 control chromosomes in the GnomAD database, including 2,278 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 0.075 ( 1126 hom., cov: 32)

Exomes 𝑓: 0.018 ( 1152 hom. )

Consequence

CD180
NM_005582.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.57

Publications

7 publications found

Variant links:

Genes affected

CD180 (HGNC:6726): (CD180 molecule) CD180 is a cell surface molecule consisting of extracellular leucine-rich repeats (LRR) and a short cytoplasmic tail. The extracellular LRR is associated with a molecule called MD-1 and form the cell surface receptor complex, RP105/MD-1. It belongs to the family of pathogen receptors, Toll-like receptors (TLR). RP105/MD1, by working in concert with TLR4, controls B cell recognition and signaling of lipopolysaccharide (LPS), a membrane constituent of Gram-negative bacteria. [provided by RefSeq, Jul 2008]

CD180 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP7

Synonymous conserved (PhyloP=-3.57 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
CD180	NM_005582.3 link	c.1482C>T	p.Thr494Thr	synonymous_variant	Exon 3 of 3	ENST00000256447.5	NP_005573.2
CD180	XM_005248504.5 link	c.1443C>T	p.Thr481Thr	synonymous_variant	Exon 4 of 4		XP_005248561.1
CD180	XM_047417178.1 link	c.1443C>T	p.Thr481Thr	synonymous_variant	Exon 4 of 4		XP_047273134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD180	ENST00000256447.5 link	c.1482C>T	p.Thr494Thr	synonymous_variant	Exon 3 of 3	1	NM_005582.3	ENSP00000256447.4

Frequencies

GnomAD3 genomes

AF:

0.0749

AC:

11393

AN:

152068

Hom.:

1125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0325

Gnomad ASJ

AF:

0.00720

Gnomad EAS

AF:

0.0271

Gnomad SAS

AF:

0.0321

Gnomad FIN

AF:

0.0276

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00932

Gnomad OTH

AF:

0.0537

GnomAD2 exomes

AF:

0.0304

AC:

7648

AN:

251382

AF XY:

0.0270

show subpopulations

Gnomad AFR exome

AF:

0.236

Gnomad AMR exome

AF:

0.0164

Gnomad ASJ exome

AF:

0.00725

Gnomad EAS exome

AF:

0.0310

Gnomad FIN exome

AF:

0.0264

Gnomad NFE exome

AF:

0.00943

Gnomad OTH exome

AF:

0.0197

GnomAD4 exome

AF:

0.0175

AC:

25627

AN:

1461876

Hom.:

1152

Cov.:

AF XY:

0.0170

AC XY:

12380

AN XY:

727240

show subpopulations

African (AFR)

AF:

0.244

AC:

8174

AN:

33480

American (AMR)

AF:

0.0172

AC:

769

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.00792

AC:

207

AN:

26134

East Asian (EAS)

AF:

0.0296

AC:

1176

AN:

39700

South Asian (SAS)

AF:

0.0268

AC:

2315

AN:

86256

European-Finnish (FIN)

AF:

0.0268

AC:

1429

AN:

53412

Middle Eastern (MID)

AF:

0.0220

AC:

127

AN:

5768

European-Non Finnish (NFE)

AF:

0.00893

AC:

9925

AN:

1112010

Other (OTH)

AF:

0.0249

AC:

1505

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

1442

2884

4327

5769

7211

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

542

1084

1626

2168

2710

<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:

0.0749

AC:

11406

AN:

152186

Hom.:

1126

Cov.:

AF XY:

0.0747

AC XY:

5558

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.230

AC:

9541

AN:

41476

American (AMR)

AF:

0.0324

AC:

496

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00720

AC:

AN:

3472

East Asian (EAS)

AF:

0.0272

AC:

141

AN:

5182

South Asian (SAS)

AF:

0.0320

AC:

154

AN:

4820

European-Finnish (FIN)

AF:

0.0276

AC:

293

AN:

10614

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00932

AC:

634

AN:

68016

Other (OTH)

AF:

0.0536

AC:

113

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

465

931

1396

1862

2327

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0311

Hom.:

578

Bravo

AF:

0.0821

Asia WGS

AF:

0.0550

AC:

192

AN:

3478

EpiCase

AF:

0.00932

EpiControl

AF:

0.0101

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.12

(source)

DANN

Benign

0.29

PhyloP100

-3.6

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over