Variant 3-112974798-TAAG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBS1BS2

The NM_138806.4(CD200R1):c.57_59delCTT(p.Phe19del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00633 in 1,608,910 control chromosomes in the GnomAD database, including 75 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 9 hom., cov: 32)

Exomes 𝑓: 0.0065 ( 66 hom. )

Consequence

CD200R1
NM_138806.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.45

Variant links:

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]

CD200R1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_138806.4. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 3-112974798-TAAG-T is Benign according to our data. Variant chr3-112974798-TAAG-T is described in ClinVar as [Benign]. Clinvar id is 3387829.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.00653 (9510/1456628) while in subpopulation SAS AF= 0.0169 (1458/86126). AF 95% confidence interval is 0.0162. There are 66 homozygotes in gnomad4_exome. There are 5020 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD200R1	NM_138806.4 linkuse as main transcript	c.57_59delCTT	p.Phe19del	disruptive_inframe_deletion	1/8	ENST00000308611.8	NP_620161.1	Q8TD46-4
CD200R1	NM_170780.3 linkuse as main transcript	c.57_59delCTT	p.Phe19del	disruptive_inframe_deletion	1/7		NP_740750.1	Q8TD46-1
CD200R1	NM_138939.3 linkuse as main transcript	c.57_59delCTT	p.Phe19del	disruptive_inframe_deletion	1/4		NP_620385.1	Q8TD46-2
CD200R1	NM_138940.3 linkuse as main transcript	c.57_59delCTT	p.Phe19del	disruptive_inframe_deletion	1/3		NP_620386.1	Q8TD46-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD200R1	ENST00000308611.8 linkuse as main transcript	c.57_59delCTT	p.Phe19del	disruptive_inframe_deletion	1/8	1	NM_138806.4	ENSP00000311035.3		Q8TD46-4

Frequencies

GnomAD3 genomes

AF:

0.00446

AC:

679

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000845

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00321

Gnomad ASJ

AF:

0.00665

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0166

Gnomad FIN

AF:

0.000753

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00694

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00631

AC:

1580

AN:

250540

Hom.:

AF XY:

0.00714

AC XY:

967

AN XY:

135498

show subpopulations

Gnomad AFR exome

AF:

0.000616

Gnomad AMR exome

AF:

0.00212

Gnomad ASJ exome

AF:

0.00745

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0160

Gnomad FIN exome

AF:

0.00102

Gnomad NFE exome

AF:

0.00778

Gnomad OTH exome

AF:

0.00491

GnomAD4 exome

AF:

0.00653

AC:

9510

AN:

1456628

Hom.:

AF XY:

0.00692

AC XY:

5020

AN XY:

724940

show subpopulations

Gnomad4 AFR exome

AF:

0.000690

Gnomad4 AMR exome

AF:

0.00265

Gnomad4 ASJ exome

AF:

0.00671

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0169

Gnomad4 FIN exome

AF:

0.00114

Gnomad4 NFE exome

AF:

0.00660

Gnomad4 OTH exome

AF:

0.00528

GnomAD4 genome

AF:

0.00445

AC:

677

AN:

152282

Hom.:

Cov.:

AF XY:

0.00442

AC XY:

329

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.000843

Gnomad4 AMR

AF:

0.00320

Gnomad4 ASJ

AF:

0.00665

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0162

Gnomad4 FIN

AF:

0.000753

Gnomad4 NFE

AF:

0.00694

Gnomad4 OTH

AF:

0.00425

Alfa

AF:

0.00172

Hom.:

Bravo

AF:

0.00419

Asia WGS

AF:

0.00346

AC:

AN:

3478

EpiCase

AF:

0.00851

EpiControl

AF:

0.00824

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2024

CD200R1: PM4:Supporting, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over