rs1951784

chr9-121114173-A-G

Variant summary

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

The NM_007018.6(CNTRL):c.1345+449A>G 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 152,164 control chromosomes in the GnomAD database, including 11,899 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 (11899 hom., cov: 33)
• Consequence: CNTRL NM_007018.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTRL	NM_007018.6	c.1345+449A>G		intron_variant		ENST00000373855.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTRL	ENST00000373855.7	c.1345+449A>G		intron_variant		5	NM_007018.6

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53906 AN: 152046 Hom.: 11887 Cov.: 33

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.483

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: 53917 AN: 152164 Hom.: 11899 Cov.: 33 AF XY: 0.364 AC XY: 27106 AN XY: 74398

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.402

Alfa AF: 0.426 Hom.: 7753

Bravo AF: 0.342

Asia WGS AF: 0.538 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.61
Dann	Benign	0.77

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: rs1951784; hg19: chr9-123876451; COSMIC: COSV53045112; COSMIC: COSV53045112;