chr3-112962738-A-G

Variant names:

• chr3-112962738-A-G
• rs1488193
• NM_138806.4:c.67+12053T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138806.4(CD200R1):​c.67+12053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 152,244 control chromosomes in the GnomAD database, including 63,146 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 0.91 (63146 hom., cov: 32)
• Consequence: CD200R1 NM_138806.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 6 publications found

Genes affected

CD200R1 (HGNC:24235): (CD200 receptor 1) This gene encodes a receptor for the OX-2 membrane glycoprotein. Both the receptor and substrate are cell surface glycoproteins containing two immunoglobulin-like domains. This receptor is restricted to the surfaces of myeloid lineage cells and the receptor-substrate interaction may function as a myeloid downregulatory signal. Mouse studies of a related gene suggest that this interaction may control myeloid function in a tissue-specific manner. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD200R1	NM_138806.4	c.67+12053T>C		intron_variant	Intron 1 of 7	ENST00000308611.8	NP_620161.1
CD200R1	NM_170780.3	c.67+12053T>C		intron_variant	Intron 1 of 6		NP_740750.1
CD200R1	NM_138939.3	c.67+12053T>C		intron_variant	Intron 1 of 3		NP_620385.1
CD200R1	NM_138940.3	c.67+12053T>C		intron_variant	Intron 1 of 2		NP_620386.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD200R1	ENST00000308611.8	c.67+12053T>C		intron_variant	Intron 1 of 7	1	NM_138806.4	ENSP00000311035.3

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138335 AN: 152126 Hom.: 63108 Cov.: 32

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.909 AC: 138429 AN: 152244 Hom.: 63146 Cov.: 32 AF XY: 0.904 AC XY: 67263 AN XY: 74426

African (AFR) AF: 0.917 AC: 38112 AN: 41544

American (AMR) AF: 0.914 AC: 13979 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3173 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3745 AN: 5176

South Asian (SAS) AF: 0.898 AC: 4334 AN: 4824

European-Finnish (FIN) AF: 0.824 AC: 8711 AN: 10578

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63361 AN: 68034

Other (OTH) AF: 0.923 AC: 1949 AN: 2112

Alfa AF: 0.926 Hom.: 191710

Bravo AF: 0.914

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.52
DANN	Benign	0.48
PhyloP100		-0.51
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: rs1488193; hg19: chr3-112681585;