9-121144526-G-T

Variant names:

• chr9-121144526-G-T
• rs12683062
• NM_007018.6:c.3052-317G>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.3052-317G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0825 in 152,272 control chromosomes in the GnomAD database, including 559 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 0.083 (559 hom., cov: 32)
• Consequence: CNTRL NM_007018.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTRL	NM_007018.6	MANE Select	c.3052-317G>T		intron	N/A	NP_008949.4
	CNTRL	NM_001330762.2		c.1396-317G>T		intron	N/A	NP_001317691.1
	CNTRL	NM_001369892.1		c.1396-317G>T		intron	N/A	NP_001356821.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTRL	ENST00000373855.7	TSL:5 MANE Select	c.3052-317G>T		intron	N/A	ENSP00000362962.1
	CNTRL	ENST00000373847.6	TSL:1	c.3052-317G>T		intron	N/A	ENSP00000362953.2
	CNTRL	ENST00000686219.1		c.1402-317G>T		intron	N/A	ENSP00000509692.1

Frequencies

GnomAD3 genomes AF: 0.0825 AC: 12558 AN: 152154 Hom.: 559 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.0907

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0692

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

GnomAD4 genome AF: 0.0825 AC: 12566 AN: 152272 Hom.: 559 Cov.: 32 AF XY: 0.0805 AC XY: 5993 AN XY: 74448

African (AFR) AF: 0.0567 AC: 2357 AN: 41554

American (AMR) AF: 0.0685 AC: 1048 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3470

East Asian (EAS) AF: 0.0322 AC: 167 AN: 5186

South Asian (SAS) AF: 0.0908 AC: 438 AN: 4824

European-Finnish (FIN) AF: 0.0700 AC: 743 AN: 10610

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7409 AN: 68012

Other (OTH) AF: 0.0685 AC: 145 AN: 2116

Alfa AF: 0.0859 Hom.: 103

Bravo AF: 0.0805

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.60
PhyloP100		-0.13
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: rs12683062; hg19: chr9-123906804;