rs2884041

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000427478.7(CNEP1R1):​c.98-835C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,024 control chromosomes in the GnomAD database, including 45,679 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 0.77 ( 45679 hom., cov: 31)

Consequence

CNEP1R1
ENST00000427478.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12
Variant links:
Genes affected
CNEP1R1 (HGNC:26759): (CTD nuclear envelope phosphatase 1 regulatory subunit 1) This gene encodes a transmembrane protein that belongs to the Tmemb_18A family. A similar protein in yeast is a component of an endoplasmic reticulum-associated protein phosphatase complex and is thought to play a role in the synthesis of triacylglycerol. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CNEP1R1NM_001281789.2 linkuse as main transcriptc.98-835C>T intron_variant ENST00000427478.7 NP_001268718.1
CNEP1R1NM_153261.6 linkuse as main transcriptc.149-835C>T intron_variant NP_694993.2
CNEP1R1NR_104042.2 linkuse as main transcriptn.239+2423C>T intron_variant, non_coding_transcript_variant
CNEP1R1NR_104043.2 linkuse as main transcriptn.188+2423C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CNEP1R1ENST00000427478.7 linkuse as main transcriptc.98-835C>T intron_variant 1 NM_001281789.2 ENSP00000394224 P1Q8N9A8-1

Frequencies

GnomAD3 genomes
AF:
0.773
AC:
117463
AN:
151906
Hom.:
45661
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.701
Gnomad AMI
AF:
0.798
Gnomad AMR
AF:
0.816
Gnomad ASJ
AF:
0.717
Gnomad EAS
AF:
0.897
Gnomad SAS
AF:
0.815
Gnomad FIN
AF:
0.798
Gnomad MID
AF:
0.772
Gnomad NFE
AF:
0.794
Gnomad OTH
AF:
0.763
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.773
AC:
117523
AN:
152024
Hom.:
45679
Cov.:
31
AF XY:
0.775
AC XY:
57568
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.701
Gnomad4 AMR
AF:
0.817
Gnomad4 ASJ
AF:
0.717
Gnomad4 EAS
AF:
0.897
Gnomad4 SAS
AF:
0.816
Gnomad4 FIN
AF:
0.798
Gnomad4 NFE
AF:
0.794
Gnomad4 OTH
AF:
0.765
Alfa
AF:
0.780
Hom.:
6780
Bravo
AF:
0.770
Asia WGS
AF:
0.831
AC:
2886
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.40
DANN
Benign
0.56

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

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

Other links and lift over

dbSNP: rs2884041; hg19: chr16-50062801; API