3-112803126-G-C

Variant names:

• chr3-112803126-G-C
• rs4682429
• ENST00000496067.2:n.232G>C

Variant summary

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

The ENST00000496067.2(CD200R1L-AS1):​n.232G>C variant causes a non coding transcript exon 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-AS1 ENST00000496067.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 5 publications found

Genes affected

CD200R1L-AS1 (HGNC:54071): (CD200R1L antisense RNA 1)

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=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD200R1L-AS1	NR_149026.1	n.232G>C		non_coding_transcript_exon_variant	Exon 2 of 5
CD200R1L-AS1	NR_149027.1	n.171+478G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD200R1L-AS1	ENST00000496067.2	n.232G>C		non_coding_transcript_exon_variant	Exon 2 of 3	5
CD200R1L-AS1	ENST00000519700.1	n.114G>C		non_coding_transcript_exon_variant	Exon 2 of 2	4
CD200R1L-AS1	ENST00000769851.1	n.64-165G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.80
PhyloP100		-0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4682429; hg19: chr3-112521973;