rs1885167

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-17514517-A-G
• chr9-17514517-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTLN	XR_007061321.1	n.4346+4496A>G		intron_variant	Intron 26 of 26
CNTLN	XR_007061322.1	n.4343+4496A>G		intron_variant	Intron 26 of 26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;