3-112336992-A-T

Variant names:

• chr3-112336992-A-T
• rs10511311
• NM_005944.7:c.12+3768A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005944.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD200	NM_005944.7	MANE Select	c.12+3768A>T		intron	N/A	NP_005935.4
	CD200	NM_001004196.4		c.87+975A>T		intron	N/A	NP_001004196.2
	CD200	NM_001365851.2		c.12+3768A>T		intron	N/A	NP_001352780.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD200	ENST00000315711.12	TSL:1 MANE Select	c.12+3768A>T		intron	N/A	ENSP00000312766.8
	CD200	ENST00000498096.6	TSL:1	n.12+3768A>T		intron	N/A	ENSP00000418576.1
	CD200	ENST00000473539.5	TSL:2	c.87+975A>T		intron	N/A	ENSP00000420298.1

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

African (AFR) AF: 0.135 AC: 5594 AN: 41356

American (AMR) AF: 0.295 AC: 4496 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3470

East Asian (EAS) AF: 0.137 AC: 706 AN: 5164

South Asian (SAS) AF: 0.158 AC: 758 AN: 4806

European-Finnish (FIN) AF: 0.322 AC: 3372 AN: 10462

Middle Eastern (MID) AF: 0.362 AC: 105 AN: 290

European-Non Finnish (NFE) AF: 0.368 AC: 24965 AN: 67914

Other (OTH) AF: 0.321 AC: 677 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.15
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10511311; hg19: chr3-112055839;