Variant chr22-17538986-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001290047.2(CECR2):c.1369-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,612,074 control chromosomes in the GnomAD database, including 187 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0081 ( 5 hom., cov: 33)

Exomes 𝑓: 0.013 ( 182 hom. )

Consequence

CECR2
NM_001290047.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.387

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 22-17538986-C-T is Benign according to our data. Variant chr22-17538986-C-T is described in ClinVar as [Benign]. Clinvar id is 790383.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0129 (18861/1459884) while in subpopulation NFE AF= 0.0156 (17373/1110838). AF 95% confidence interval is 0.0154. There are 182 homozygotes in gnomad4_exome. There are 9144 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1226 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CECR2	NM_001290047.2 linkuse as main transcript	c.1369-7C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000262608.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CECR2	ENST00000262608.13 linkuse as main transcript	c.1369-7C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_001290047.2	P2	Q9BXF3-3
	ENST00000651475.1 linkuse as main transcript	n.334+3895G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00807

AC:

1227

AN:

152072

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00481

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00695

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0129

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00751

AC:

1865

AN:

248214

Hom.:

AF XY:

0.00769

AC XY:

1036

AN XY:

134648

show subpopulations

Gnomad AFR exome

AF:

0.00439

Gnomad AMR exome

AF:

0.00551

Gnomad ASJ exome

AF:

0.000100

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00480

Gnomad FIN exome

AF:

0.00182

Gnomad NFE exome

AF:

0.0122

Gnomad OTH exome

AF:

0.00813

GnomAD4 exome

AF:

0.0129

AC:

18861

AN:

1459884

Hom.:

182

Cov.:

AF XY:

0.0126

AC XY:

9144

AN XY:

726196

show subpopulations

Gnomad4 AFR exome

AF:

0.00329

Gnomad4 AMR exome

AF:

0.00501

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00469

Gnomad4 FIN exome

AF:

0.00201

Gnomad4 NFE exome

AF:

0.0156

Gnomad4 OTH exome

AF:

0.0105

GnomAD4 genome

AF:

0.00806

AC:

1226

AN:

152190

Hom.:

Cov.:

AF XY:

0.00717

AC XY:

533

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.00479

Gnomad4 AMR

AF:

0.00694

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.00151

Gnomad4 NFE

AF:

0.0129

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00974

Hom.:

Bravo

AF:

0.00843

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.0124

EpiControl

AF:

0.0127

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

Labcorp Genetics (formerly Invitae), Labcorp

Jul 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.2

DANN

Benign

0.19

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