22-17473581-A-T

Position:

• chr22-17473581-A-T

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CECR2	NM_001290047.2	c.127-4007A>T		intron_variant		ENST00000262608.13	NP_001276976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CECR2	ENST00000262608.13	c.127-4007A>T		intron_variant		1	NM_001290047.2	ENSP00000262608.11
CECR2	ENST00000400585.7	c.-363-4007A>T		intron_variant		1		ENSP00000383428.2
CECR2	ENST00000342247.10	c.127-4007A>T		intron_variant		5		ENSP00000341219.6
CECR2	ENST00000497534.1	n.269-4007A>T		intron_variant		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

Gnomad4 AFR AF: 0.0775

Gnomad4 AMR AF: 0.0668

Gnomad4 ASJ AF: 0.0821

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.0762

Gnomad4 FIN AF: 0.0779

Gnomad4 NFE AF: 0.0937

Gnomad4 OTH AF: 0.0866

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2097596; hg19: chr22-17952623;