22-17553499-A-G

Position:

• chr22-17553499-A-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CECR2	NM_001290047.2	c.*659A>G		3_prime_UTR_variant	19/19	ENST00000262608.13	NP_001276976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CECR2	ENST00000262608.13	c.*659A>G		3_prime_UTR_variant	19/19	1	NM_001290047.2	ENSP00000262608	P2
	ENST00000651475.1	n.102-7448T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68848 AN: 151746 Hom.: 16063 Cov.: 31

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: 70 AN: 132 Hom.: 20 Cov.: 0 AF XY: 0.565 AC XY: 52 AN XY: 92

Gnomad4 AFR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.583

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.454 AC: 68877 AN: 151864 Hom.: 16058 Cov.: 31 AF XY: 0.455 AC XY: 33755 AN XY: 74214

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.464

Alfa AF: 0.503 Hom.: 26507

Bravo AF: 0.444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs174345; hg19: chr22-18033199;