dbSNP rs2058710: CMKLR2-AS:n.310+537A>G (chr2-206257058-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000644292.1(CMKLR2-AS):n.310+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
ENST00000644292.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0510

Publications

10 publications found

Variant links:

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]

CMKLR2-AS links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMKLR2-AS	NR_104359.1 link	n.658+537A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CMKLR2-AS	ENST00000644292.1 link	n.310+537A>G	intron_variant	Intron 3 of 4
CMKLR2-AS	ENST00000648653.1 link	n.491+537A>G	intron_variant	Intron 4 of 5
CMKLR2-AS	ENST00000771999.1 link	n.489+537A>G	intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34065

AN:

151844

Hom.:

4298

Cov.:

show subpopulations

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.:

AF XY:

0.226

AC XY:

16812

AN XY:

74278

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.261

AC:

17731

AN:

67946

Other (OTH)

AF:

0.233

AC:

489

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1330

2660

3990

5320

6650

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

352

704

1056

1408

1760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

4.0

(source)

DANN

Benign

0.62

PhyloP100

0.051

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over