3-112345110-C-T

Variant names:

• chr3-112345110-C-T
• rs141880997
• NM_005944.7:c.243C>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_005944.7(CD200):​c.243C>T​(p.Asn81Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CD200 NM_005944.7 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 3 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP7: Synonymous conserved (PhyloP=-1.57 with no splicing effect.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD200	NM_005944.7	MANE Select	c.243C>T	p.Asn81Asn	synonymous	Exon 3 of 6	NP_005935.4
	CD200	NM_001004196.4		c.318C>T	p.Asn106Asn	synonymous	Exon 4 of 7	NP_001004196.2	P41217-3
	CD200	NM_001365851.2		c.243C>T	p.Asn81Asn	synonymous	Exon 3 of 5	NP_001352780.1	P41217-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD200	ENST00000315711.12	TSL:1 MANE Select	c.243C>T	p.Asn81Asn	synonymous	Exon 3 of 6	ENSP00000312766.8	P41217-2
	CD200	ENST00000498096.6	TSL:1	n.243C>T		non_coding_transcript_exon	Exon 3 of 6	ENSP00000418576.1	F8WC99
	CD200	ENST00000473539.5	TSL:2	c.318C>T	p.Asn106Asn	synonymous	Exon 4 of 7	ENSP00000420298.1	P41217-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.44
DANN	Benign	0.41
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

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: rs141880997; hg19: chr3-112063957; COSMIC: COSV105136090; COSMIC: COSV105136090;