22-39123191-T-C

Position:

• chr22-39123191-T-C

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CBX7	ENST00000475962.5	n.45-2618A>G		intron_variant, non_coding_transcript_variant		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;