Genetic Variant CECR2:c.*659A>G (chr22-17553499-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001290047.2(CECR2):c.*659A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,864 control chromosomes in the GnomAD database, including 16,058 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 0.45 ( 16058 hom., cov: 31)

Exomes 𝑓: 0.53 ( 20 hom. )

Failed GnomAD Quality Control

Consequence

CECR2
NM_001290047.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.693

Publications

9 publications found

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:

ENSG00000286195 (HGNC:):

ENSG00000286195 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001290047.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CECR2	NM_001290047.2	MANE Select	c.*659A>G		3_prime_UTR	Exon 19 of 19	NP_001276976.1
	CECR2	NM_001290046.2		c.*659A>G		3_prime_UTR	Exon 19 of 19	NP_001276975.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CECR2	ENST00000262608.13	TSL:1 MANE Select	c.*659A>G	3_prime_UTR	Exon 19 of 19	ENSP00000262608.11
CECR2	ENST00000400585.7	TSL:1	c.*659A>G	3_prime_UTR	Exon 19 of 19	ENSP00000383428.2
CECR2	ENST00000355219.4	TSL:2	n.*853A>G	non_coding_transcript_exon	Exon 4 of 4	ENSP00000347357.3

Frequencies

GnomAD3 genomes

AF:

0.454

AC:

68848

AN:

151746

Hom.:

16063

Cov.:

show subpopulations

Gnomad AFR

AF:

0.348

Gnomad AMI

AF:

0.697

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.413

Gnomad SAS

AF:

0.555

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.590

Gnomad NFE

AF:

0.510

Gnomad OTH

AF:

0.467

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.530

AC:

AN:

132

Hom.:

Cov.:

AF XY:

0.565

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.583

AC:

AN:

108

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.572

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.454

AC:

68877

AN:

151864

Hom.:

16058

Cov.:

AF XY:

0.455

AC XY:

33755

AN XY:

74214

show subpopulations

African (AFR)

AF:

0.348

AC:

14410

AN:

41396

American (AMR)

AF:

0.431

AC:

6570

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.499

AC:

1730

AN:

3468

East Asian (EAS)

AF:

0.413

AC:

2127

AN:

5156

South Asian (SAS)

AF:

0.554

AC:

2669

AN:

4816

European-Finnish (FIN)

AF:

0.471

AC:

4965

AN:

10536

Middle Eastern (MID)

AF:

0.579

AC:

168

AN:

290

European-Non Finnish (NFE)

AF:

0.510

AC:

34625

AN:

67924

Other (OTH)

AF:

0.464

AC:

979

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1891

3782

5674

7565

9456

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

642

1284

1926

2568

3210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.493

Hom.:

37582

Bravo

AF:

0.444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.30

(source)

PhyloP100

-0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over