rs2058708

Positions:

• chr2-206217239-G-T

Variant summary

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

The ENST00000407325.6(CMKLR2):​c.-148+570C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 152,150 control chromosomes in the GnomAD database, including 545 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 0.078 (545 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CMKLR2 ENST00000407325.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404

Genes affected

CMKLR2 (HGNC:4463): (chemerin chemokine-like receptor 2) Enables adipokinetic hormone binding activity and adipokinetic hormone receptor activity. Predicted to be involved in glucose homeostasis and neuropeptide signaling pathway. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMKLR2-AS	NR_104359.1	n.302+13562G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMKLR2-AS	ENST00000648653.1	n.135+13562G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11811 AN: 152032 Hom.: 545 Cov.: 32

Gnomad AFR AF: 0.0444

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.0342

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0776 AC: 11813 AN: 152150 Hom.: 545 Cov.: 32 AF XY: 0.0780 AC XY: 5806 AN XY: 74392

Gnomad4 AFR AF: 0.0444

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.0342

Gnomad4 SAS AF: 0.0955

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0992

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0920 Hom.: 412

Bravo AF: 0.0694

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2058708; hg19: chr2-207081963;