dbSNP rs2228443: ATP5POP1:n.109T>C (chr2-206236763-A-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000445875.1(ATP5POP1):n.109T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ATP5POP1
ENST00000445875.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.236

Publications

1 publications found

Variant links:

Genes affected

ATP5POP1 (HGNC:54673): (ATP5PO pseudogene 1)

ATP5POP1 links:

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445875.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMKLR2-AS	NR_104359.1		n.303-3680A>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ATP5POP1	ENST00000445875.1	TSL:6	n.109T>C	non_coding_transcript_exon	Exon 1 of 1
CMKLR2-AS	ENST00000644292.1		n.101-19103A>G	intron	N/A
CMKLR2-AS	ENST00000648653.1		n.136-3680A>G	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

740202

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

390968

African (AFR)

AF:

0.00

AC:

AN:

19256

American (AMR)

AF:

0.00

AC:

AN:

40678

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18106

East Asian (EAS)

AF:

0.00

AC:

AN:

25410

South Asian (SAS)

AF:

0.00

AC:

AN:

72872

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35864

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3912

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

490840

Other (OTH)

AF:

0.00

AC:

AN:

33264

GnomAD4 genome

Cov.:

Alfa

AF:

0.0468

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.6

(source)

DANN

Benign

0.44

PhyloP100

0.24

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over