rs894379

Variant names:

• chr9-17454595-G-A
• rs894379
• NM_017738.4:c.3115-2929G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-17454595-G-A
• chr9-17454595-G-C
• chr9-17454595-G-T

Variant summary

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

The NM_017738.4(CNTLN):​c.3115-2929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,122 control chromosomes in the GnomAD database, including 43,220 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 0.75 (43220 hom., cov: 33)
• Consequence: CNTLN NM_017738.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017738.4. 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
	CNTLN	NM_017738.4	MANE Select	c.3115-2929G>A		intron	N/A	NP_060208.2
	CNTLN	NM_001365029.1		c.3112-2929G>A		intron	N/A	NP_001351958.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTLN	ENST00000380647.8	TSL:1 MANE Select	c.3115-2929G>A		intron	N/A	ENSP00000370021.3
	CNTLN	ENST00000461247.1	TSL:3	n.339-2929G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114244 AN: 152004 Hom.: 43154 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.752 AC: 114370 AN: 152122 Hom.: 43220 Cov.: 33 AF XY: 0.752 AC XY: 55920 AN XY: 74358

African (AFR) AF: 0.788 AC: 32719 AN: 41504

American (AMR) AF: 0.754 AC: 11512 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2175 AN: 3470

East Asian (EAS) AF: 0.908 AC: 4706 AN: 5182

South Asian (SAS) AF: 0.629 AC: 3030 AN: 4814

European-Finnish (FIN) AF: 0.768 AC: 8109 AN: 10562

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.731 AC: 49735 AN: 68002

Other (OTH) AF: 0.741 AC: 1564 AN: 2112

Alfa AF: 0.676 Hom.: 2188

Bravo AF: 0.758

Asia WGS AF: 0.791 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.53
PhyloP100		0.17
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: rs894379; hg19: chr9-17454593;