ENST00000475962.5:n.45-2618A>G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CBX7	ENST00000475962.5	n.45-2618A>G		intron_variant	Intron 1 of 1	3

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

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.517

Alfa AF: 0.462 Hom.: 21305

Bravo AF: 0.571

Asia WGS AF: 0.426 AC: 1484 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	1.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs139371; hg19: chr22-39519196;