Variant 3-112827472-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001199215.3(CD200R1L):c.262G>C(p.Asp88His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000752 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000075 ( 0 hom. )

Consequence

CD200R1L
NM_001199215.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.04

Variant links:

Genes affected

CD200R1L (HGNC:24665): (CD200 receptor 1 like) Predicted to enable signaling receptor activity. Predicted to be involved in regulation of neuroinflammatory response. Predicted to be integral component of membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

CD200R1L links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.28983146).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD200R1L	NM_001199215.3 linkuse as main transcript	c.262G>C	p.Asp88His	missense_variant	5/8	ENST00000488794.6	NP_001186144.1	Q6Q8B3-2
CD200R1L	NM_001008784.4 linkuse as main transcript	c.325G>C	p.Asp109His	missense_variant	4/7		NP_001008784.2	Q6Q8B3-1
CD200R1L	NM_001370552.3 linkuse as main transcript	c.262G>C	p.Asp88His	missense_variant	6/9		NP_001357481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CD200R1L	ENST00000488794.6 linkuse as main transcript	c.262G>C	p.Asp88His	missense_variant	5/8	5	NM_001199215.3	ENSP00000418413.1	Q6Q8B3-2
CD200R1L	ENST00000398214.5 linkuse as main transcript	c.325G>C	p.Asp109His	missense_variant	3/6	1		ENSP00000381272.1	Q6Q8B3-1
CD200R1L	ENST00000486723.1 linkuse as main transcript	n.*324G>C		non_coding_transcript_exon_variant	5/8	2		ENSP00000420461.1	F8WDF0
CD200R1L	ENST00000486723.1 linkuse as main transcript	n.*324G>C		3_prime_UTR_variant	5/8	2		ENSP00000420461.1	F8WDF0

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000159

AC:

AN:

251462

Hom.:

AF XY:

0.0000221

AC XY:

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000752

AC:

AN:

1461884

Hom.:

Cov.:

AF XY:

0.00000825

AC XY:

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 20, 2021

The c.325G>C (p.D109H) alteration is located in exon 3 (coding exon 3) of the CD200R1L gene. This alteration results from a G to C substitution at nucleotide position 325, causing the aspartic acid (D) at amino acid position 109 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.017

T;.;.;.

Eigen

Benign

-0.64

Eigen_PC

Benign

-0.85

FATHMM_MKL

Benign

0.021

LIST_S2

Benign

0.70

T;T;T;T

M_CAP

Benign

0.0051

MetaRNN

Benign

0.29

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.5

L;.;.;.

PrimateAI

Benign

0.23

PROVEAN

Uncertain

-2.9

D;D;D;.

REVEL

Benign

0.050

Sift

Benign

0.085

T;T;T;.

Sift4G

Benign

0.079

T;T;T;T

Polyphen

0.95

P;.;.;.

Vest4

0.060

MutPred

0.33

Loss of stability (P = 0.0883);.;.;.;

MVP

0.33

MPC

0.046

ClinPred

0.73

GERP RS

-1.4

Varity_R

0.086

gMVP

0.39

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.17

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