chr3-112803126-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000496067.2(CD200R1L-AS1):​n.232G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,150 control chromosomes in the GnomAD database, including 11,244 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 0.37 (11243 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000496067.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD200R1L-AS1	NR_149026.1		n.232G>A		non_coding_transcript_exon	Exon 2 of 5
	CD200R1L-AS1	NR_149027.1		n.171+478G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD200R1L-AS1	ENST00000496067.2	TSL:5	n.232G>A		non_coding_transcript_exon	Exon 2 of 3
	CD200R1L-AS1	ENST00000519700.1	TSL:4	n.114G>A		non_coding_transcript_exon	Exon 2 of 2
	CD200R1L-AS1	ENST00000769851.1		n.64-165G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56992 AN: 152030 Hom.: 11235 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.0833

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.407

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.375 AC: 57029 AN: 152148 Hom.: 11243 Cov.: 32 AF XY: 0.371 AC XY: 27610 AN XY: 74376

African (AFR) AF: 0.289 AC: 11980 AN: 41494

American (AMR) AF: 0.362 AC: 5538 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1584 AN: 3470

East Asian (EAS) AF: 0.0833 AC: 432 AN: 5184

South Asian (SAS) AF: 0.415 AC: 1998 AN: 4814

European-Finnish (FIN) AF: 0.409 AC: 4330 AN: 10578

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29820 AN: 68004

Other (OTH) AF: 0.409 AC: 864 AN: 2114

Alfa AF: 0.416 Hom.: 58624

Bravo AF: 0.366

Asia WGS AF: 0.296 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.79
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;