2-65065628-G-T

Variant names:

• chr2-65065628-G-T
• rs2080385
• NM_015147.3:c.-46-3771G>T

Variant summary

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

The NM_015147.3(CEP68):​c.-46-3771G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,058 control chromosomes in the GnomAD database, including 6,869 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 0.29 (6869 hom., cov: 32)
• Consequence: CEP68 NM_015147.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 7 publications found

Genes affected

CEP68 (HGNC:29076): (centrosomal protein 68) Enables protein domain specific binding activity and protein kinase binding activity. Involved in centriole-centriole cohesion and protein localization to organelle. Located in several cellular components, including centriolar satellite; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015147.3. 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
	CEP68	NM_015147.3	MANE Select	c.-46-3771G>T		intron	N/A	NP_055962.2	Q76N32-1
	CEP68	NM_001319100.2		c.-46-3771G>T		intron	N/A	NP_001306029.1	Q76N32-1
	CEP68	NM_001410838.1		c.-46-3771G>T		intron	N/A	NP_001397767.1	A0A994J4E5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP68	ENST00000377990.7	TSL:1 MANE Select	c.-46-3771G>T		intron	N/A	ENSP00000367229.2	Q76N32-1
	CEP68	ENST00000260569.4	TSL:1	c.-46-3771G>T		intron	N/A	ENSP00000260569.4	Q76N32-2
	CEP68	ENST00000537589.1	TSL:1	n.74-5826G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44476 AN: 151940 Hom.: 6838 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.293 AC: 44558 AN: 152058 Hom.: 6869 Cov.: 32 AF XY: 0.292 AC XY: 21669 AN XY: 74312

African (AFR) AF: 0.376 AC: 15562 AN: 41442

American (AMR) AF: 0.278 AC: 4245 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1719 AN: 5170

South Asian (SAS) AF: 0.313 AC: 1512 AN: 4826

European-Finnish (FIN) AF: 0.209 AC: 2214 AN: 10568

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16969 AN: 67982

Other (OTH) AF: 0.324 AC: 685 AN: 2112

Alfa AF: 0.284 Hom.: 781

Bravo AF: 0.302

Asia WGS AF: 0.393 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.24
PhyloP100		-1.3
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: rs2080385; hg19: chr2-65292762;