chr9-17161529-G-T

Position:

• chr9-17161529-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017738.4(CNTLN):​c.449+18153G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,096 control chromosomes in the GnomAD database, including 2,600 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 0.18 (2600 hom., cov: 32)
• Consequence: CNTLN NM_017738.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

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]

CNTLN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTLN	NM_017738.4	c.449+18153G>T		intron_variant		ENST00000380647.8	NP_060208.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTLN	ENST00000380647.8	c.449+18153G>T		intron_variant		1	NM_017738.4	ENSP00000370021.3
CNTLN	ENST00000380641.4	c.449+18153G>T		intron_variant		2		ENSP00000370015.3
CNTLN	ENST00000484374.1	n.534-5289G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27686 AN: 151976 Hom.: 2599 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.182 AC: 27690 AN: 152096 Hom.: 2600 Cov.: 32 AF XY: 0.183 AC XY: 13619 AN XY: 74372

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.177

Alfa AF: 0.154 Hom.: 1810

Bravo AF: 0.188

Asia WGS AF: 0.237 AC: 820 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.5
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511633; hg19: chr9-17161527;