Variant 11-10751502-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014633.5(CTR9):c.45+45G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 1,588,700 control chromosomes in the GnomAD database, including 124,340 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 9931 hom., cov: 31)

Exomes 𝑓: 0.39 ( 114409 hom. )

Consequence

CTR9
NM_014633.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.37

Variant links:

Genes affected

CTR9 (HGNC:16850): (CTR9 homolog, Paf1/RNA polymerase II complex component) The protein encoded by this gene is a component of the PAF1 complex, which associates with RNA polymerase II and functions in transcriptional regulation and elongation. This complex also plays a role in the modification of histones. [provided by RefSeq, Oct 2016]

CTR9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 11-10751502-G-A is Benign according to our data. Variant chr11-10751502-G-A is described in ClinVar as [Benign]. Clinvar id is 1271533.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTR9	NM_014633.5 linkuse as main transcript	c.45+45G>A		intron_variant		ENST00000361367.7
CTR9	NM_001346279.2 linkuse as main transcript	c.45+45G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTR9	ENST00000361367.7 linkuse as main transcript	c.45+45G>A		intron_variant		1	NM_014633.5	P1
CTR9	ENST00000524523.1 linkuse as main transcript	c.6+45G>A		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

53023

AN:

151754

Hom.:

9921

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.350

Gnomad AMR

AF:

0.298

Gnomad ASJ

AF:

0.463

Gnomad EAS

AF:

0.514

Gnomad SAS

AF:

0.479

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.357

Gnomad NFE

AF:

0.399

Gnomad OTH

AF:

0.334

GnomAD3 exomes

AF:

0.391

AC:

92949

AN:

237786

Hom.:

18973

AF XY:

0.401

AC XY:

51879

AN XY:

129512

show subpopulations

Gnomad AFR exome

AF:

0.220

Gnomad AMR exome

AF:

0.255

Gnomad ASJ exome

AF:

0.477

Gnomad EAS exome

AF:

0.517

Gnomad SAS exome

AF:

0.475

Gnomad FIN exome

AF:

0.422

Gnomad NFE exome

AF:

0.400

Gnomad OTH exome

AF:

0.397

GnomAD4 exome

AF:

0.395

AC:

567249

AN:

1436826

Hom.:

114409

Cov.:

AF XY:

0.399

AC XY:

285511

AN XY:

715536

show subpopulations

Gnomad4 AFR exome

AF:

0.222

Gnomad4 AMR exome

AF:

0.261

Gnomad4 ASJ exome

AF:

0.470

Gnomad4 EAS exome

AF:

0.536

Gnomad4 SAS exome

AF:

0.477

Gnomad4 FIN exome

AF:

0.422

Gnomad4 NFE exome

AF:

0.391

Gnomad4 OTH exome

AF:

0.389

GnomAD4 genome

AF:

0.349

AC:

53054

AN:

151874

Hom.:

9931

Cov.:

AF XY:

0.353

AC XY:

26162

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.463

Gnomad4 EAS

AF:

0.513

Gnomad4 SAS

AF:

0.480

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.399

Gnomad4 OTH

AF:

0.339

Alfa

AF:

0.380

Hom.:

3543

Bravo

AF:

0.331

Asia WGS

AF:

0.474

AC:

1646

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

DANN

Benign

0.88

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