22-17051559-G-A

Variant names:

• chr22-17051559-G-A
• rs2845384
• ENST00000441006.6:n.1006+4133G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000813089.1(ENSG00000290931):​n.382G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,196 control chromosomes in the GnomAD database, including 53,562 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 0.83 (53562 hom., cov: 32)
• Consequence: ENSG00000290931 ENST00000813089.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 3 publications found

Genes affected

ENSG00000290931 (HGNC:):

CECR7 (HGNC:1845): (cat eye syndrome chromosome region, candidate 7)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813089.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CECR7	NR_015352.2		n.1006+4133G>A		intron	N/A
	CECR7	NR_152825.1		n.1006+4133G>A		intron	N/A
	CECR7	NR_152826.1		n.1006+4133G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290931	ENST00000441006.6	TSL:1	n.1006+4133G>A		intron	N/A
	ENSG00000290931	ENST00000813089.1		n.382G>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000290931	ENST00000414401.5	TSL:4	n.364+4133G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126570 AN: 152078 Hom.: 53512 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.832 AC: 126673 AN: 152196 Hom.: 53562 Cov.: 32 AF XY: 0.829 AC XY: 61672 AN XY: 74406

African (AFR) AF: 0.960 AC: 39906 AN: 41558

American (AMR) AF: 0.659 AC: 10067 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2819 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2996 AN: 5162

South Asian (SAS) AF: 0.762 AC: 3671 AN: 4816

European-Finnish (FIN) AF: 0.843 AC: 8932 AN: 10600

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55499 AN: 67986

Other (OTH) AF: 0.813 AC: 1719 AN: 2114

Alfa AF: 0.841 Hom.: 8181

Bravo AF: 0.821

Asia WGS AF: 0.664 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		-0.75
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs2845384; hg19: chr22-17532449;