rs4682429

chr3-112803126-G-Achr3-112803126-G-Cchr3-112803126-G-T

Variant summary

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

The NR_149026.1(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 NR_149026.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD200R1L-AS1	NR_149026.1	n.232G>A		non_coding_transcript_exon_variant	2/5
CD200R1L-AS1	NR_149027.1	n.171+478G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD200R1L-AS1	ENST00000496067.2	n.232G>A		non_coding_transcript_exon_variant	2/3	5
CD200R1L-AS1	ENST00000519700.1	n.114G>A		non_coding_transcript_exon_variant	2/2	4

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

Gnomad4 AFR exome AF: 1.00

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

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.0833

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.409

Alfa AF: 0.424 Hom.: 28907

Bravo AF: 0.366

Asia WGS AF: 0.296 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4682429; hg19: chr3-112521973;