rs16982400

Positions:

• chr22-17418497-T-C

Variant summary

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

The NM_001290047.2(CECR2):​c.126+48588T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,092 control chromosomes in the GnomAD database, including 4,220 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 0.20 (4220 hom., cov: 32)
• Consequence: CECR2 NM_001290047.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CECR2	NM_001290047.2	c.126+48588T>C		intron_variant		ENST00000262608.13	NP_001276976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CECR2	ENST00000262608.13	c.126+48588T>C		intron_variant		1	NM_001290047.2	ENSP00000262608.11
CECR2	ENST00000400585.7	c.-364+58474T>C		intron_variant		1		ENSP00000383428.2
CECR2	ENST00000342247.10	c.126+48588T>C		intron_variant		5		ENSP00000341219.6

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30455 AN: 151974 Hom.: 4202 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.201 AC: 30521 AN: 152092 Hom.: 4220 Cov.: 32 AF XY: 0.198 AC XY: 14713 AN XY: 74368

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0642

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.173

Alfa AF: 0.130 Hom.: 2621

Bravo AF: 0.208

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs16982400; hg19: chr22-17897544;