Variant rs7184114 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_016284.5(CNOT1):c.3201+124G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 1,247,326 control chromosomes in the GnomAD database, including 287,708 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.70 ( 38211 hom., cov: 32)

Exomes 𝑓: 0.67 ( 249497 hom. )

Consequence

CNOT1
NM_016284.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.287

Variant links:

Genes affected

CNOT1 (HGNC:7877): (CCR4-NOT transcription complex subunit 1) Enables armadillo repeat domain binding activity; molecular adaptor activity; and nuclear receptor binding activity. Contributes to poly(A)-specific ribonuclease activity. Involved in several processes, including negative regulation of signal transduction; positive regulation of cytoplasmic mRNA processing body assembly; and regulation of gene expression. Located in P-body and cytosol. Part of CCR4-NOT complex. Implicated in holoprosencephaly. [provided by Alliance of Genome Resources, Apr 2022]

CNOT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 16-58551465-C-A is Benign according to our data. Variant chr16-58551465-C-A is described in ClinVar as [Benign]. Clinvar id is 1250890.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
CNOT1	NM_016284.5 linkuse as main transcript	c.3201+124G>T	intron_variant	ENST00000317147.10	NP_057368.3
CNOT1	NM_001265612.2 linkuse as main transcript	c.3186+124G>T	intron_variant		NP_001252541.1
CNOT1	NM_206999.3 linkuse as main transcript	c.3201+124G>T	intron_variant		NP_996882.1
CNOT1	NR_049763.2 linkuse as main transcript	n.3459+124G>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNOT1	ENST00000317147.10 linkuse as main transcript	c.3201+124G>T		intron_variant		1	NM_016284.5	ENSP00000320949	P3	A5YKK6-1

Frequencies

GnomAD3 genomes

AF:

0.703

AC:

106855

AN:

151962

Hom.:

38176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.829

Gnomad AMI

AF:

0.698

Gnomad AMR

AF:

0.603

Gnomad ASJ

AF:

0.651

Gnomad EAS

AF:

0.617

Gnomad SAS

AF:

0.587

Gnomad FIN

AF:

0.642

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.676

Gnomad OTH

AF:

0.703

GnomAD4 exome

AF:

0.672

AC:

735603

AN:

1095246

Hom.:

249497

AF XY:

0.670

AC XY:

367056

AN XY:

548158

show subpopulations

Gnomad4 AFR exome

AF:

0.840

Gnomad4 AMR exome

AF:

0.527

Gnomad4 ASJ exome

AF:

0.644

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.591

Gnomad4 FIN exome

AF:

0.645

Gnomad4 NFE exome

AF:

0.682

Gnomad4 OTH exome

AF:

0.667

GnomAD4 genome

AF:

0.703

AC:

106935

AN:

152080

Hom.:

38211

Cov.:

AF XY:

0.697

AC XY:

51845

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.829

Gnomad4 AMR

AF:

0.602

Gnomad4 ASJ

AF:

0.651

Gnomad4 EAS

AF:

0.618

Gnomad4 SAS

AF:

0.586

Gnomad4 FIN

AF:

0.642

Gnomad4 NFE

AF:

0.676

Gnomad4 OTH

AF:

0.700

Alfa

AF:

0.688

Hom.:

4800

Bravo

AF:

0.708

Asia WGS

AF:

0.621

AC:

2157

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

6.2

DANN

Benign

0.25

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over