chr5-67180023-T-A

Position:

• chr5-67180023-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_005582.3(CD180):​c.*2834A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,172 control chromosomes in the GnomAD database, including 5,060 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 (5060 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CD180 NM_005582.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD180	NM_005582.3	c.*2834A>T		3_prime_UTR_variant	3/3	ENST00000256447.5
CD180	XM_005248504.5	c.*2834A>T		3_prime_UTR_variant	4/4
CD180	XM_047417178.1	c.*2834A>T		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD180	ENST00000256447.5	c.*2834A>T		3_prime_UTR_variant	3/3	1	NM_005582.3	P1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30338 AN: 152054 Hom.: 5030 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0698

Gnomad OTH AF: 0.178

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.200 AC: 30427 AN: 152172 Hom.: 5060 Cov.: 33 AF XY: 0.201 AC XY: 14948 AN XY: 74388

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.0698

Gnomad4 OTH AF: 0.182

Alfa AF: 0.143 Hom.: 358

Bravo AF: 0.222

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	13
DANN	Benign	0.82

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: rs6890674; hg19: chr5-66475851;