rs10511311

chr3-112336992-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+3768A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,718 control chromosomes in the GnomAD database, including 6,734 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 0.28 (6734 hom., cov: 30)
• Consequence: CD200 NM_005944.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD200	NM_005944.7	c.12+3768A>T		intron_variant		ENST00000315711.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD200	ENST00000315711.12	c.12+3768A>T		intron_variant		1	NM_005944.7	P1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42323 AN: 151600 Hom.: 6737 Cov.: 30

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.279 AC: 42335 AN: 151718 Hom.: 6734 Cov.: 30 AF XY: 0.273 AC XY: 20249 AN XY: 74092

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.321

Alfa AF: 0.312 Hom.: 996

Bravo AF: 0.275

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.7
Dann	Benign	0.15

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: rs10511311; hg19: chr3-112055839;