22-17473581-A-T

Variant names:

• chr22-17473581-A-T
• rs2097596
• NM_001290047.2:c.127-4007A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001290047.2(CECR2):​c.127-4007A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0868 in 152,288 control chromosomes in the GnomAD database, including 607 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 0.087 (607 hom., cov: 32)
• Consequence: CECR2 NM_001290047.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CECR2	NM_001290047.2	c.127-4007A>T		intron_variant	Intron 1 of 18	ENST00000262608.13	NP_001276976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CECR2	ENST00000262608.13	c.127-4007A>T		intron_variant	Intron 1 of 18	1	NM_001290047.2	ENSP00000262608.11
CECR2	ENST00000400585.7	c.-363-4007A>T		intron_variant	Intron 1 of 18	1		ENSP00000383428.2
CECR2	ENST00000342247.10	c.127-4007A>T		intron_variant	Intron 1 of 19	5		ENSP00000341219.6
CECR2	ENST00000497534.1	n.269-4007A>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0869 AC: 13225 AN: 152170 Hom.: 611 Cov.: 32

Gnomad AFR AF: 0.0777

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.0846

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0868 AC: 13222 AN: 152288 Hom.: 607 Cov.: 32 AF XY: 0.0847 AC XY: 6310 AN XY: 74458

African (AFR) AF: 0.0775 AC: 3221 AN: 41562

American (AMR) AF: 0.0668 AC: 1022 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 285 AN: 3472

East Asian (EAS) AF: 0.163 AC: 843 AN: 5180

South Asian (SAS) AF: 0.0762 AC: 368 AN: 4830

European-Finnish (FIN) AF: 0.0779 AC: 827 AN: 10612

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0937 AC: 6374 AN: 68018

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0351 Hom.: 36

Bravo AF: 0.0850

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.38
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2097596; hg19: chr22-17952623;