GeneBe

ENST00000445875.1:n.109T>C

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.236
Variant links:
Genes affected
ATP5POP1 (HGNC:54673): (ATP5PO pseudogene 1)
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATP5POP1 n.206236763A>G intragenic_variant
CMKLR2-ASNR_104359.1 linkn.303-3680A>G intron_variant Intron 1 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATP5POP1ENST00000445875.1 linkn.109T>C non_coding_transcript_exon_variant Exon 1 of 1 6
CMKLR2-ASENST00000644292.1 linkn.101-19103A>G intron_variant Intron 1 of 4
CMKLR2-ASENST00000648653.1 linkn.136-3680A>G intron_variant Intron 1 of 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
740202
Hom.:
0
Cov.:
10
AF XY:
0.00
AC XY:
0
AN XY:
390968
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0477
Hom.:
10

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.6
DANN
Benign
0.44

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2228443; hg19: chr2-207101487; API