rs4682103

chr3-112336946-A-Gchr3-112336946-A-T

Variant summary

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

The NM_005944.7(CD200):c.12+3722A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,908 control chromosomes in the GnomAD database, including 26,099 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 0.58 (26099 hom., cov: 30)
• Consequence: CD200 NM_005944.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

Genes affected

CD200 (HGNC:7203): (CD200 molecule) This gene encodes a type I membrane glycoprotein containing two extracellular immunoglobulin domains, a transmembrane and a cytoplasmic domain. This gene is expressed by various cell types, including B cells, a subset of T cells, thymocytes, endothelial cells, and neurons. The encoded protein plays an important role in immunosuppression and regulation of anti-tumor activity. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD200	NM_005944.7	c.12+3722A>G		intron_variant		ENST00000315711.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD200	ENST00000315711.12	c.12+3722A>G		intron_variant		1	NM_005944.7	P1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88306 AN: 151790 Hom.: 26053 Cov.: 30

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.582 AC: 88407 AN: 151908 Hom.: 26099 Cov.: 30 AF XY: 0.587 AC XY: 43577 AN XY: 74240

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.564

Alfa AF: 0.552 Hom.: 32116

Bravo AF: 0.584

Asia WGS AF: 0.770 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.0
Dann	Benign	0.88

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: rs4682103; hg19: chr3-112055793;