rs1317244

Positions:

• chr3-112334718-G-A

Variant summary

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

The NM_005944.7(CD200):​c.12+1494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,322 control chromosomes in the GnomAD database, including 9,837 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 0.36 (9837 hom., cov: 31)
• Consequence: CD200 NM_005944.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD200	NM_005944.7	c.12+1494G>A		intron_variant		ENST00000315711.12	NP_005935.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD200	ENST00000315711.12	c.12+1494G>A		intron_variant		1	NM_005944.7	ENSP00000312766	P1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54099 AN: 151204 Hom.: 9824 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.358 AC: 54144 AN: 151322 Hom.: 9837 Cov.: 31 AF XY: 0.361 AC XY: 26632 AN XY: 73858

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.346

Alfa AF: 0.361 Hom.: 16610

Bravo AF: 0.347

Asia WGS AF: 0.412 AC: 1429 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.65

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: rs1317244; hg19: chr3-112053565; COSMIC: COSV59864533; COSMIC: COSV59864533;