rs174345

Variant names:

• chr22-17553499-A-G
• rs174345
• NM_001290047.2:c.*659A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-17553499-A-G
• chr22-17553499-A-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.*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
• Publications: 9 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]

ENSG00000286195 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CECR2	NM_001290047.2	c.*659A>G		3_prime_UTR_variant	Exon 19 of 19	ENST00000262608.13	NP_001276976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CECR2	ENST00000262608.13	c.*659A>G		3_prime_UTR_variant	Exon 19 of 19	1	NM_001290047.2	ENSP00000262608.11

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

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 0.250 AC: 2 AN: 8

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.583 AC: 63 AN: 108

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.348 AC: 14410 AN: 41396

American (AMR) AF: 0.431 AC: 6570 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1730 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2127 AN: 5156

South Asian (SAS) AF: 0.554 AC: 2669 AN: 4816

European-Finnish (FIN) AF: 0.471 AC: 4965 AN: 10536

Middle Eastern (MID) AF: 0.579 AC: 168 AN: 290

European-Non Finnish (NFE) AF: 0.510 AC: 34625 AN: 67924

Other (OTH) AF: 0.464 AC: 979 AN: 2108

Alfa AF: 0.493 Hom.: 37582

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs174345; hg19: chr22-18033199;