chr5-618471-A-G

Variant names:

• chr5-618471-A-G
• rs7726839
• NM_018140.4:c.83-519A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018140.4(CEP72):​c.83-519A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,168 control chromosomes in the GnomAD database, including 8,411 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 0.31 (8411 hom., cov: 33)
• Consequence: CEP72 NM_018140.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 25 publications found

Genes affected

CEP72 (HGNC:25547): (centrosomal protein 72) The product of this gene is a member of the leucine-rich-repeat (LRR) superfamily of proteins. The protein is localized to the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018140.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP72	NM_018140.4	MANE Select	c.83-519A>G		intron	N/A	NP_060610.2	Q9P209-1
	CEP72	NR_164122.1		n.263-519A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP72	ENST00000264935.6	TSL:1 MANE Select	c.83-519A>G		intron	N/A	ENSP00000264935.5	Q9P209-1
	CEP72	ENST00000856935.1		c.83-519A>G		intron	N/A	ENSP00000526994.1
	CEP72	ENST00000919286.1		c.83-519A>G		intron	N/A	ENSP00000589345.1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46602 AN: 152050 Hom.: 8378 Cov.: 33

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0373

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.307 AC: 46682 AN: 152168 Hom.: 8411 Cov.: 33 AF XY: 0.299 AC XY: 22280 AN XY: 74398

African (AFR) AF: 0.502 AC: 20817 AN: 41462

American (AMR) AF: 0.279 AC: 4265 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3470

East Asian (EAS) AF: 0.0374 AC: 194 AN: 5192

South Asian (SAS) AF: 0.231 AC: 1117 AN: 4826

European-Finnish (FIN) AF: 0.158 AC: 1675 AN: 10596

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16910 AN: 68012

Other (OTH) AF: 0.276 AC: 583 AN: 2112

Alfa AF: 0.264 Hom.: 10552

Bravo AF: 0.322

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.72
DANN	Benign	0.72
PhyloP100		-0.72
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: rs7726839; hg19: chr5-618586;