rs5744478

Positions:

• chr5-67193737-A-G

Variant summary

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

The NM_005582.3(CD180):​c.90+2815T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 152,336 control chromosomes in the GnomAD database, including 290 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 0.055 (290 hom., cov: 32)
• Consequence: CD180 NM_005582.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD180	NM_005582.3	c.90+2815T>C		intron_variant		ENST00000256447.5	NP_005573.2
CD180	XM_005248504.5	c.-106-2646T>C		intron_variant			XP_005248561.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD180	ENST00000256447.5	c.90+2815T>C		intron_variant		1	NM_005582.3	ENSP00000256447.4

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 8426 AN: 152218 Hom.: 290 Cov.: 32

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0553 AC: 8429 AN: 152336 Hom.: 290 Cov.: 32 AF XY: 0.0560 AC XY: 4168 AN XY: 74488

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0532

Gnomad4 ASJ AF: 0.0758

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0749

Gnomad4 FIN AF: 0.0835

Gnomad4 NFE AF: 0.0785

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0746 Hom.: 238

Bravo AF: 0.0501

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.71

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: rs5744478; hg19: chr5-66489565;