Variant 22-17542187-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001290047.2(CECR2):c.2044C>A(p.Pro682Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000381 in 1,612,134 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0016 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00026 ( 1 hom. )

Consequence

CECR2
NM_001290047.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.65

Variant links:

Genes affected

CECR2 (HGNC:1840): (CECR2 histone acetyl-lysine reader) This gene encodes a bromodomain-containing protein that is involved in chromatin remodeling, and may additionally play a role in DNA damage response. The encoded protein functions as part of an ATP-dependent complex that is involved in neurulation. This gene is a candidate gene for Cat Eye Syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

CECR2 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0041348934).

BP6

Variant 22-17542187-C-A is Benign according to our data. Variant chr22-17542187-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 717121.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 238 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CECR2	NM_001290047.2 linkuse as main transcript	c.2044C>A	p.Pro682Thr	missense_variant	16/19	ENST00000262608.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CECR2	ENST00000262608.13 linkuse as main transcript	c.2044C>A	p.Pro682Thr	missense_variant	16/19	1	NM_001290047.2	P2	Q9BXF3-3
	ENST00000651475.1 linkuse as main transcript	n.334+694G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00155

AC:

236

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00502

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000103

Gnomad OTH

AF:

0.000958

GnomAD3 exomes

AF:

0.000506

AC:

125

AN:

247150

Hom.:

AF XY:

0.000403

AC XY:

AN XY:

134038

show subpopulations

Gnomad AFR exome

AF:

0.00585

Gnomad AMR exome

AF:

0.000438

Gnomad ASJ exome

AF:

0.000301

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000134

Gnomad OTH exome

AF:

0.000499

GnomAD4 exome

AF:

0.000258

AC:

377

AN:

1459834

Hom.:

Cov.:

AF XY:

0.000231

AC XY:

168

AN XY:

725858

show subpopulations

Gnomad4 AFR exome

AF:

0.00598

Gnomad4 AMR exome

AF:

0.000359

Gnomad4 ASJ exome

AF:

0.000230

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000101

Gnomad4 OTH exome

AF:

0.000531

GnomAD4 genome

AF:

0.00156

AC:

238

AN:

152300

Hom.:

Cov.:

AF XY:

0.00145

AC XY:

108

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00505

Gnomad4 AMR

AF:

0.00105

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000103

Gnomad4 OTH

AF:

0.000948

Alfa

AF:

0.000395

Hom.:

Bravo

AF:

0.00178

ESP6500AA

AF:

0.00504

AC:

ESP6500EA

AF:

0.000120

AC:

ExAC

AF:

0.000546

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.098

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.97

Eigen

Benign

-0.19

Eigen_PC

Benign

-0.084

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.73

T;T;T;T

M_CAP

Benign

0.0054

MetaRNN

Benign

0.0041

T;T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

0.94

D;D

PrimateAI

Benign

0.30

PROVEAN

Uncertain

-2.5

D;.;.;.

REVEL

Benign

0.041

Sift

Benign

0.12

T;.;.;.

Sift4G

Benign

0.080

T;D;T;D

Polyphen

0.0020

B;B;.;.

Vest4

0.22

MVP

0.37

ClinPred

0.0070

GERP RS

4.2

Varity_R

0.061

gMVP

0.26

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