chr3-112837546-T-C

Position:

• chr3-112837546-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199215.3(CD200R1L):​c.-18+396A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,198 control chromosomes in the GnomAD database, including 999 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 0.11 (999 hom., cov: 32)
• Consequence: CD200R1L NM_001199215.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD200R1L	NM_001199215.3	c.-18+396A>G		intron_variant		ENST00000488794.6	NP_001186144.1
CD200R1L	NM_001008784.4	c.46+8133A>G		intron_variant			NP_001008784.2
CD200R1L	NM_001370552.3	c.-18+396A>G		intron_variant			NP_001357481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD200R1L	ENST00000488794.6	c.-18+396A>G		intron_variant		5	NM_001199215.3	ENSP00000418413.1
CD200R1L	ENST00000398214.5	c.46+8133A>G		intron_variant		1		ENSP00000381272.1
CD200R1L	ENST00000486723.1	n.*45+396A>G		intron_variant		2		ENSP00000420461.1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17170 AN: 152080 Hom.: 997 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0747

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.113 AC: 17195 AN: 152198 Hom.: 999 Cov.: 32 AF XY: 0.112 AC XY: 8326 AN XY: 74424

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.0870

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0747

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.104

Alfa AF: 0.103 Hom.: 1379

Bravo AF: 0.112

Asia WGS AF: 0.161 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs16860145; hg19: chr3-112556393;