chr3-112837546-T-C

Variant names:

• chr3-112837546-T-C
• rs16860145
• NM_001199215.3:c.-18+396A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199215.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD200R1L	NM_001199215.3	MANE Select	c.-18+396A>G		intron	N/A	NP_001186144.1	Q6Q8B3-2
	CD200R1L	NM_001008784.4		c.46+8133A>G		intron	N/A	NP_001008784.2	Q6Q8B3-1
	CD200R1L	NM_001370552.3		c.-18+396A>G		intron	N/A	NP_001357481.1	Q6Q8B3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD200R1L	ENST00000488794.6	TSL:5 MANE Select	c.-18+396A>G		intron	N/A	ENSP00000418413.1	Q6Q8B3-2
	CD200R1L	ENST00000398214.5	TSL:1	c.46+8133A>G		intron	N/A	ENSP00000381272.1	Q6Q8B3-1
	CD200R1L	ENST00000486723.1	TSL:2	n.*45+396A>G		intron	N/A	ENSP00000420461.1	F8WDF0

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

African (AFR) AF: 0.140 AC: 5812 AN: 41510

American (AMR) AF: 0.0702 AC: 1074 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3470

East Asian (EAS) AF: 0.190 AC: 980 AN: 5170

South Asian (SAS) AF: 0.164 AC: 789 AN: 4824

European-Finnish (FIN) AF: 0.0747 AC: 792 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7034 AN: 67998

Other (OTH) AF: 0.104 AC: 219 AN: 2114

Alfa AF: 0.106 Hom.: 3326

Bravo AF: 0.112

Asia WGS AF: 0.161 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.72
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: rs16860145; hg19: chr3-112556393;