rs2058710

Positions:

• chr2-206257058-A-G

Variant summary

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

The NR_104359.1(CMKLR2-AS):​n.658+537A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,962 control chromosomes in the GnomAD database, including 4,305 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 0.22 (4305 hom., cov: 32)
• Consequence: CMKLR2-AS NR_104359.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

Genes affected

CMKLR2-AS (HGNC:48602): (CMKLR2 antisense RNA) This gene is thought to produce a non-coding RNA. It is situated adjacent to a differentially methylated region (DMR) and is imprinted and paternally expressed in the placenta. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CMKLR2-AS	NR_104359.1	n.658+537A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMKLR2-AS	ENST00000648653.1	n.491+537A>G		intron_variant, non_coding_transcript_variant
CMKLR2-AS	ENST00000644292.1	n.310+537A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34065 AN: 151844 Hom.: 4298 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.224 AC: 34103 AN: 151962 Hom.: 4305 Cov.: 32 AF XY: 0.226 AC XY: 16812 AN XY: 74278

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.233

Alfa AF: 0.255 Hom.: 10392

Bravo AF: 0.224

Asia WGS AF: 0.212 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2058710; hg19: chr2-207121782;