9-121076879-G-C

Variant names:

• chr9-121076879-G-C
• rs7856420
• NM_007018.6:c.-205+1812G>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.-205+1812G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 151,320 control chromosomes in the GnomAD database, including 30,022 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 0.61 (30022 hom., cov: 30)
• Consequence: CNTRL NM_007018.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTRL	NM_007018.6	c.-205+1812G>C		intron_variant	Intron 1 of 43	ENST00000373855.7	NP_008949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTRL	ENST00000373855.7	c.-205+1812G>C		intron_variant	Intron 1 of 43	5	NM_007018.6	ENSP00000362962.1

Frequencies

GnomAD3 genomes AF: 0.614 AC: 92864 AN: 151202 Hom.: 30003 Cov.: 30

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.614 AC: 92925 AN: 151320 Hom.: 30022 Cov.: 30 AF XY: 0.621 AC XY: 45889 AN XY: 73948

African (AFR) AF: 0.399 AC: 16453 AN: 41252

American (AMR) AF: 0.739 AC: 11250 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2346 AN: 3464

East Asian (EAS) AF: 0.767 AC: 3935 AN: 5128

South Asian (SAS) AF: 0.894 AC: 4306 AN: 4816

European-Finnish (FIN) AF: 0.632 AC: 6604 AN: 10452

Middle Eastern (MID) AF: 0.701 AC: 202 AN: 288

European-Non Finnish (NFE) AF: 0.677 AC: 45802 AN: 67688

Other (OTH) AF: 0.645 AC: 1359 AN: 2106

Alfa AF: 0.624 Hom.: 3657

Bravo AF: 0.614

Asia WGS AF: 0.770 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.85
PhyloP100		0.66
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: rs7856420; hg19: chr9-123839157;