NM_005944.7:c.12+3722A>G

Variant names:

• chr3-112336946-A-G
• rs4682103
• NM_005944.7:c.12+3722A>G

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+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
• Publications: 7 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=-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 rank	MANE	Protein	UniProt
CD200	NM_005944.7	c.12+3722A>G		intron_variant	Intron 1 of 5	ENST00000315711.12	NP_005935.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD200	ENST00000315711.12	c.12+3722A>G		intron_variant	Intron 1 of 5	1	NM_005944.7	ENSP00000312766.8

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

African (AFR) AF: 0.620 AC: 25670 AN: 41390

American (AMR) AF: 0.585 AC: 8929 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3468

East Asian (EAS) AF: 0.826 AC: 4262 AN: 5158

South Asian (SAS) AF: 0.759 AC: 3654 AN: 4816

European-Finnish (FIN) AF: 0.542 AC: 5702 AN: 10524

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36339 AN: 67958

Other (OTH) AF: 0.564 AC: 1192 AN: 2112

Alfa AF: 0.553 Hom.: 43359

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
PhyloP100		-0.27
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: rs4682103; hg19: chr3-112055793;