chr5-67185241-G-T

Variant names:

• chr5-67185241-G-T
• rs1697143
• NM_005582.3:c.257+610C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005582.3(CD180):​c.257+610C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 141,720 control chromosomes in the GnomAD database, including 3,591 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 0.20 (3591 hom., cov: 27)
• Consequence: CD180 NM_005582.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005582.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD180	NM_005582.3	MANE Select	c.257+610C>A		intron	N/A	NP_005573.2	Q99467

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD180	ENST00000256447.5	TSL:1 MANE Select	c.257+610C>A		intron	N/A	ENSP00000256447.4	Q99467
	CD180	ENST00000515027.1	TSL:2	n.447+610C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 28967 AN: 141656 Hom.: 3587 Cov.: 27

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.270

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.204 AC: 28967 AN: 141720 Hom.: 3591 Cov.: 27 AF XY: 0.201 AC XY: 13757 AN XY: 68600

African (AFR) AF: 0.0583 AC: 2136 AN: 36660

American (AMR) AF: 0.212 AC: 2961 AN: 13938

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 462 AN: 3436

East Asian (EAS) AF: 0.116 AC: 536 AN: 4614

South Asian (SAS) AF: 0.158 AC: 699 AN: 4416

European-Finnish (FIN) AF: 0.257 AC: 2253 AN: 8762

Middle Eastern (MID) AF: 0.266 AC: 59 AN: 222

European-Non Finnish (NFE) AF: 0.287 AC: 19143 AN: 66812

Other (OTH) AF: 0.207 AC: 407 AN: 1968

Alfa AF: 0.243 Hom.: 7409

Bravo AF: 0.182

Asia WGS AF: 0.100 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.56
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1697143; hg19: chr5-66481069;