rs7350278

Variant names:

• chr9-17524040-G-T
• rs7350278
• XR_007061321.1:n.4347-4348G>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.4347-4348G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,160 control chromosomes in the GnomAD database, including 3,455 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 0.19 (3455 hom., cov: 33)
• Consequence: CNTLN XR_007061321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.187 AC: 28415 AN: 152042 Hom.: 3458 Cov.: 33

Gnomad AFR AF: 0.0563

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.187 AC: 28410 AN: 152160 Hom.: 3455 Cov.: 33 AF XY: 0.183 AC XY: 13628 AN XY: 74392

African (AFR) AF: 0.0561 AC: 2331 AN: 41538

American (AMR) AF: 0.170 AC: 2597 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3468

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5176

South Asian (SAS) AF: 0.160 AC: 773 AN: 4820

European-Finnish (FIN) AF: 0.223 AC: 2358 AN: 10574

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18214 AN: 67966

Other (OTH) AF: 0.224 AC: 473 AN: 2114

Alfa AF: 0.246 Hom.: 20958

Bravo AF: 0.176

Asia WGS AF: 0.0920 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs7350278; hg19: chr9-17524038;