rs2058710

Variant names:

• chr2-206257058-A-G
• rs2058710
• ENST00000644292.1:n.310+537A>G

Variant summary

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

The NR_104359.1(CMKLR2-AS):​n.658+537A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_104359.1. 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
	CMKLR2-AS	NR_104359.1		n.658+537A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMKLR2-AS	ENST00000644292.1		n.310+537A>G		intron	N/A
	CMKLR2-AS	ENST00000648653.1		n.491+537A>G		intron	N/A
	CMKLR2-AS	ENST00000771999.1		n.489+537A>G		intron	N/A

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

African (AFR) AF: 0.125 AC: 5176 AN: 41492

American (AMR) AF: 0.327 AC: 4988 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3470

East Asian (EAS) AF: 0.193 AC: 991 AN: 5140

South Asian (SAS) AF: 0.193 AC: 928 AN: 4800

European-Finnish (FIN) AF: 0.252 AC: 2660 AN: 10552

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17731 AN: 67946

Other (OTH) AF: 0.233 AC: 489 AN: 2102

Alfa AF: 0.248 Hom.: 15636

Bravo AF: 0.224

Asia WGS AF: 0.212 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs2058710; hg19: chr2-207121782;