9-121107237-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTRL	NM_007018.6	c.809-565T>C		intron_variant	Intron 7 of 43	ENST00000373855.7	NP_008949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTRL	ENST00000373855.7	c.809-565T>C		intron_variant	Intron 7 of 43	5	NM_007018.6	ENSP00000362962.1

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

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.718

Alfa AF: 0.672 Hom.: 3802

Bravo AF: 0.702

Asia WGS AF: 0.891 AC: 3096 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	0.57
DANN	Benign	0.47

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: rs1998505; hg19: chr9-123869515;