XR_007061321.1:n.4346+4496A>G

Variant names:

• chr9-17514517-A-G
• rs1885167
• XR_007061321.1:n.4346+4496A>G

Variant summary

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

The XR_007061321.1(CNTLN):​n.4346+4496A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,088 control chromosomes in the GnomAD database, including 35,075 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 0.62 (35075 hom., cov: 32)
• Consequence: CNTLN XR_007061321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 4 publications found

Genes affected

CNTLN (HGNC:23432): (centlein) Enables protein domain specific binding activity; protein kinase binding activity; and protein-macromolecule adaptor activity. Involved in centriole-centriole cohesion and protein localization to organelle. Located in cytosol; microtubule organizing center; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94510 AN: 151970 Hom.: 35075 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.621 AC: 94515 AN: 152088 Hom.: 35075 Cov.: 32 AF XY: 0.628 AC XY: 46701 AN XY: 74332

African (AFR) AF: 0.187 AC: 7755 AN: 41510

American (AMR) AF: 0.763 AC: 11647 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2708 AN: 3468

East Asian (EAS) AF: 0.962 AC: 4976 AN: 5174

South Asian (SAS) AF: 0.808 AC: 3896 AN: 4820

European-Finnish (FIN) AF: 0.755 AC: 7974 AN: 10560

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53249 AN: 67976

Other (OTH) AF: 0.658 AC: 1389 AN: 2110

Alfa AF: 0.720 Hom.: 76623

Bravo AF: 0.602

Asia WGS AF: 0.816 AC: 2835 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	3.2
DANN	Benign	0.77
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs1885167; hg19: chr9-17514515; COSMIC: COSV60336233;