rs3789311

Positions:

• chr9-121176720-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007018.6(CNTRL):​c.6955-443T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,208 control chromosomes in the GnomAD database, including 1,320 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 0.13 (1320 hom., cov: 32)
• Consequence: CNTRL NM_007018.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

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

Verdict is Benign. Variant got -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 = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTRL	NM_007018.6	c.6955-443T>C		intron_variant		ENST00000373855.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTRL	ENST00000373855.7	c.6955-443T>C		intron_variant		5	NM_007018.6

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19303 AN: 152090 Hom.: 1318 Cov.: 32

Gnomad AFR AF: 0.0926

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0798

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.127 AC: 19322 AN: 152208 Hom.: 1320 Cov.: 32 AF XY: 0.126 AC XY: 9393 AN XY: 74416

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.0798

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.142

Alfa AF: 0.146 Hom.: 2241

Bravo AF: 0.134

Asia WGS AF: 0.164 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.22

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

Publications

LitVar

Other links and lift over

dbSNP: rs3789311; hg19: chr9-123938998;