rs381924

Positions:

• chr22-17522081-T-C
• chr22-17522081-T-G
• chr22-17522081-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001290047.2(CECR2):​c.955-2037T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,164 control chromosomes in the GnomAD database, including 1,961 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 0.14 (1961 hom., cov: 32)
• Consequence: CECR2 NM_001290047.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CECR2	NM_001290047.2	c.955-2037T>C		intron_variant		ENST00000262608.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CECR2	ENST00000262608.13	c.955-2037T>C		intron_variant		1	NM_001290047.2	P2
	ENST00000651475.1	n.933A>G		non_coding_transcript_exon_variant	6/6

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21435 AN: 152046 Hom.: 1962 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.0754

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.141 AC: 21449 AN: 152164 Hom.: 1961 Cov.: 32 AF XY: 0.140 AC XY: 10413 AN XY: 74396

Gnomad4 AFR AF: 0.0360

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0366

Gnomad4 SAS AF: 0.0757

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.135

Alfa AF: 0.168 Hom.: 315

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs174312; hg19: chr22-18001109;