Variant rs10516143 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001370472.1(CNOT6):c.300-84T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 864,250 control chromosomes in the GnomAD database, including 103,743 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 0.44 ( 15649 hom., cov: 31)

Exomes 𝑓: 0.49 ( 88094 hom. )

Consequence

CNOT6
NM_001370472.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.475

Variant links:

Genes affected

CNOT6 (HGNC:14099): (CCR4-NOT transcription complex subunit 6) This gene encodes the catalytic component of the CCR4-NOT core transcriptional regulation complex. The encoded protein has a 3'-5' RNase activity and prefers polyadenylated substrates. The CCR4-NOT complex plays a role in many cellular processes, including miRNA-mediated repression, mRNA degradation, and transcriptional regulation. [provided by RefSeq, Dec 2014]

CNOT6 links:

CNOT6 (HGNC:):

CNOT6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNOT6	NM_001370472.1 linkuse as main transcript	c.300-84T>A		intron_variant		ENST00000261951.9	NP_001357401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNOT6	ENST00000261951.9 linkuse as main transcript	c.300-84T>A		intron_variant		5	NM_001370472.1	ENSP00000261951.4		Q9ULM6

Frequencies

GnomAD3 genomes

AF:

0.439

AC:

66669

AN:

151824

Hom.:

15648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.422

Gnomad ASJ

AF:

0.599

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.432

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.536

Gnomad OTH

AF:

0.445

GnomAD4 exome

AF:

0.488

AC:

347476

AN:

712308

Hom.:

88094

AF XY:

0.490

AC XY:

184499

AN XY:

376554

show subpopulations

Gnomad4 AFR exome

AF:

0.285

Gnomad4 AMR exome

AF:

0.386

Gnomad4 ASJ exome

AF:

0.599

Gnomad4 EAS exome

AF:

0.198

Gnomad4 SAS exome

AF:

0.451

Gnomad4 FIN exome

AF:

0.491

Gnomad4 NFE exome

AF:

0.524

Gnomad4 OTH exome

AF:

0.480

GnomAD4 genome

AF:

0.439

AC:

66681

AN:

151942

Hom.:

15649

Cov.:

AF XY:

0.438

AC XY:

32545

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.286

Gnomad4 AMR

AF:

0.421

Gnomad4 ASJ

AF:

0.599

Gnomad4 EAS

AF:

0.231

Gnomad4 SAS

AF:

0.433

Gnomad4 FIN

AF:

0.494

Gnomad4 NFE

AF:

0.536

Gnomad4 OTH

AF:

0.439

Alfa

AF:

0.476

Hom.:

2127

Bravo

AF:

0.424

Asia WGS

AF:

0.296

AC:

1030

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.5

DANN

Benign

0.46

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over