rs10963072

Variant names:

• chr9-17378778-G-A
• rs10963072
• NM_017738.4:c.1988-9384G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-17378778-G-A
• chr9-17378778-G-C
• chr9-17378778-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.1988-9384G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,112 control chromosomes in the GnomAD database, including 3,670 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 0.21 (3670 hom., cov: 32)
• Consequence: CNTLN NM_017738.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 7 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTLN	NM_017738.4	c.1988-9384G>A		intron_variant	Intron 13 of 25	ENST00000380647.8	NP_060208.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTLN	ENST00000380647.8	c.1988-9384G>A		intron_variant	Intron 13 of 25	1	NM_017738.4	ENSP00000370021.3

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32188 AN: 151994 Hom.: 3668 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.212 AC: 32181 AN: 152112 Hom.: 3670 Cov.: 32 AF XY: 0.212 AC XY: 15729 AN XY: 74352

African (AFR) AF: 0.157 AC: 6518 AN: 41506

American (AMR) AF: 0.217 AC: 3324 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3468

East Asian (EAS) AF: 0.0864 AC: 446 AN: 5164

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4818

European-Finnish (FIN) AF: 0.213 AC: 2256 AN: 10572

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15969 AN: 67978

Other (OTH) AF: 0.231 AC: 487 AN: 2110

Alfa AF: 0.228 Hom.: 17647

Bravo AF: 0.205

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.70
PhyloP100		-1.9
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: rs10963072; hg19: chr9-17378776;