chr9-121098097-C-T

Variant names:

• chr9-121098097-C-T
• rs9657673
• NM_007018.6:c.622-289C>T

Variant summary

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

The NM_007018.6(CNTRL):​c.622-289C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,054 control chromosomes in the GnomAD database, including 11,885 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 0.35 (11885 hom., cov: 32)
• Consequence: CNTRL NM_007018.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 6 publications found

Genes affected

CNTRL (HGNC:1858): (centriolin) This gene encodes a centrosomal protein required for the centrosome to function as a microtubule organizing center. The gene product is also associated with centrosome maturation. One version of stem cell myeloproliferative disorder is the result of a reciprocal translocation between chromosomes 8 and 9, with the breakpoint associated with fibroblast growth factor receptor 1 and centrosomal protein 1. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007018.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTRL	NM_007018.6	MANE Select	c.622-289C>T		intron	N/A	NP_008949.4
	CNTRL	NM_001369893.1		c.622-289C>T		intron	N/A	NP_001356822.1	Q5JVD1
	CNTRL	NM_001369894.1		c.622-289C>T		intron	N/A	NP_001356823.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTRL	ENST00000373855.7	TSL:5 MANE Select	c.622-289C>T		intron	N/A	ENSP00000362962.1	Q7Z7A1-1
	CNTRL	ENST00000373847.6	TSL:1	c.622-289C>T		intron	N/A	ENSP00000362953.2	Q5JVD1
	CNTRL	ENST00000934490.1		c.622-289C>T		intron	N/A	ENSP00000604549.1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53873 AN: 151936 Hom.: 11873 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.354 AC: 53884 AN: 152054 Hom.: 11885 Cov.: 32 AF XY: 0.365 AC XY: 27100 AN XY: 74310

African (AFR) AF: 0.0833 AC: 3457 AN: 41500

American (AMR) AF: 0.482 AC: 7367 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1783 AN: 3472

East Asian (EAS) AF: 0.557 AC: 2879 AN: 5172

South Asian (SAS) AF: 0.644 AC: 3099 AN: 4814

European-Finnish (FIN) AF: 0.484 AC: 5100 AN: 10546

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28671 AN: 67946

Other (OTH) AF: 0.401 AC: 848 AN: 2114

Alfa AF: 0.377 Hom.: 2622

Bravo AF: 0.341

Asia WGS AF: 0.535 AC: 1860 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		-0.12
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: rs9657673; hg19: chr9-123860375; COSMIC: COSV53045047;