rs877529

Variant names:

• chr22-39146287-G-A
• rs877529
• NM_175709.5:c.113+3502C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-39146287-G-A
• chr22-39146287-G-C
• chr22-39146287-G-T

Variant summary

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

The NM_175709.5(CBX7):​c.113+3502C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,154 control chromosomes in the GnomAD database, including 13,832 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 0.42 (13832 hom., cov: 33)
• Consequence: CBX7 NM_175709.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 37 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]

ENSG00000297177 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175709.5. 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
	CBX7	NM_175709.5	MANE Select	c.113+3502C>T		intron	N/A	NP_783640.1
	CBX7	NM_001346743.2		c.113+3502C>T		intron	N/A	NP_001333672.1
	CBX7	NM_001346744.2		c.113+3502C>T		intron	N/A	NP_001333673.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CBX7	ENST00000216133.10	TSL:1 MANE Select	c.113+3502C>T		intron	N/A	ENSP00000216133.5
	CBX7	ENST00000401405.7	TSL:1	c.113+3502C>T		intron	N/A	ENSP00000384035.3
	CBX7	ENST00000434260.1	TSL:3	c.113+3502C>T		intron	N/A	ENSP00000410896.1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 64064 AN: 152036 Hom.: 13829 Cov.: 33

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.421 AC: 64078 AN: 152154 Hom.: 13832 Cov.: 33 AF XY: 0.415 AC XY: 30870 AN XY: 74378

African (AFR) AF: 0.473 AC: 19613 AN: 41506

American (AMR) AF: 0.288 AC: 4405 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1523 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1111 AN: 5184

South Asian (SAS) AF: 0.368 AC: 1778 AN: 4828

European-Finnish (FIN) AF: 0.446 AC: 4714 AN: 10580

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29537 AN: 67976

Other (OTH) AF: 0.402 AC: 848 AN: 2112

Alfa AF: 0.426 Hom.: 51258

Bravo AF: 0.412

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.93
DANN	Benign	0.48
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs877529; hg19: chr22-39542292;