chr22-39123191-T-C

Variant names:

• chr22-39123191-T-C
• rs139371
• ENST00000475962.5:n.45-2618A>G

Variant summary

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

The ENST00000475962.5(CBX7):​n.45-2618A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,056 control chromosomes in the GnomAD database, including 27,117 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 0.57 (27117 hom., cov: 31)
• Consequence: CBX7 ENST00000475962.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 20 publications found

Genes affected

CBX7 (HGNC:1557): (chromobox 7) This gene encodes a protein that contains the CHROMO (CHRomatin Organization MOdifier) domain. The encoded protein is a component of the Polycomb repressive complex 1 (PRC1), and is thought to control the lifespan of several normal human cells. [provided by RefSeq, Oct 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000475962.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CBX7	ENST00000475962.5	TSL:3	n.45-2618A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86001 AN: 151936 Hom.: 27063 Cov.: 31

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.566 AC: 86107 AN: 152056 Hom.: 27117 Cov.: 31 AF XY: 0.560 AC XY: 41638 AN XY: 74306

African (AFR) AF: 0.866 AC: 35917 AN: 41492

American (AMR) AF: 0.413 AC: 6312 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1855 AN: 5160

South Asian (SAS) AF: 0.489 AC: 2352 AN: 4814

European-Finnish (FIN) AF: 0.465 AC: 4916 AN: 10572

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31520 AN: 67958

Other (OTH) AF: 0.517 AC: 1090 AN: 2110

Alfa AF: 0.491 Hom.: 60433

Bravo AF: 0.571

Asia WGS AF: 0.426 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs139371; hg19: chr22-39519196;