chr3-112837546-T-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001199215.3(CD200R1L):​c.-18+396A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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>T		intron	N/A	NP_001186144.1	Q6Q8B3-2
	CD200R1L	NM_001008784.4		c.46+8133A>T		intron	N/A	NP_001008784.2	Q6Q8B3-1
	CD200R1L	NM_001370552.3		c.-18+396A>T		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>T		intron	N/A	ENSP00000418413.1	Q6Q8B3-2
	CD200R1L	ENST00000398214.5	TSL:1	c.46+8133A>T		intron	N/A	ENSP00000381272.1	Q6Q8B3-1
	CD200R1L	ENST00000486723.1	TSL:2	n.*45+396A>T		intron	N/A	ENSP00000420461.1	F8WDF0

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.69
PhyloP100		0.27

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;