chr9-121107237-T-C

Variant names:

• chr9-121107237-T-C
• rs1998505
• NM_007018.6:c.809-565T>C

Variant summary

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

The NM_007018.6(CNTRL):​c.809-565T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,924 control chromosomes in the GnomAD database, including 37,490 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 0.70 (37490 hom., cov: 30)
• Consequence: CNTRL NM_007018.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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.809-565T>C		intron	N/A	NP_008949.4
	CNTRL	NM_001369893.1		c.809-565T>C		intron	N/A	NP_001356822.1	Q5JVD1
	CNTRL	NM_001369894.1		c.809-565T>C		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.809-565T>C		intron	N/A	ENSP00000362962.1	Q7Z7A1-1
	CNTRL	ENST00000373847.6	TSL:1	c.809-565T>C		intron	N/A	ENSP00000362953.2	Q5JVD1
	CNTRL	ENST00000934490.1		c.809-565T>C		intron	N/A	ENSP00000604549.1

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105930 AN: 151806 Hom.: 37448 Cov.: 30

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.698 AC: 106026 AN: 151924 Hom.: 37490 Cov.: 30 AF XY: 0.702 AC XY: 52142 AN XY: 74246

African (AFR) AF: 0.624 AC: 25838 AN: 41398

American (AMR) AF: 0.774 AC: 11822 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2530 AN: 3468

East Asian (EAS) AF: 0.956 AC: 4951 AN: 5178

South Asian (SAS) AF: 0.917 AC: 4408 AN: 4808

European-Finnish (FIN) AF: 0.657 AC: 6934 AN: 10548

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47132 AN: 67938

Other (OTH) AF: 0.718 AC: 1517 AN: 2114

Alfa AF: 0.678 Hom.: 5113

Bravo AF: 0.702

Asia WGS AF: 0.891 AC: 3096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.47
PhyloP100		-0.83
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: rs1998505; hg19: chr9-123869515;