rs12621608

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015147.3(CEP68):​c.1884+638C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 161,052 control chromosomes in the GnomAD database, including 2,767 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 0.17 ( 2612 hom., cov: 32)
Exomes 𝑓: 0.18 ( 155 hom. )

Consequence

CEP68
NM_015147.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20
Variant links:
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]
RAB1A (HGNC:9758): (RAB1A, member RAS oncogene family) This gene encodes a member of the Ras superfamily of GTPases. Members of the gene family cycle between inactive GDP-bound and active GTP-bound forms. This small GTPase controls vesicle traffic from the endoplasmic reticulum to the Golgi apparatus. Multiple alternatively spliced transcript variants have been identified for this gene which encode different protein isoforms. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CEP68NM_015147.3 linkuse as main transcriptc.1884+638C>T intron_variant ENST00000377990.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CEP68ENST00000377990.7 linkuse as main transcriptc.1884+638C>T intron_variant 1 NM_015147.3 P2Q76N32-1

Frequencies

GnomAD3 genomes
AF:
0.167
AC:
25473
AN:
152136
Hom.:
2602
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0698
Gnomad AMI
AF:
0.185
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.304
Gnomad EAS
AF:
0.335
Gnomad SAS
AF:
0.287
Gnomad FIN
AF:
0.178
Gnomad MID
AF:
0.290
Gnomad NFE
AF:
0.186
Gnomad OTH
AF:
0.202
GnomAD4 exome
AF:
0.175
AC:
1541
AN:
8798
Hom.:
155
Cov.:
0
AF XY:
0.170
AC XY:
767
AN XY:
4512
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.191
Gnomad4 ASJ exome
AF:
0.283
Gnomad4 EAS exome
AF:
0.274
Gnomad4 SAS exome
AF:
0.226
Gnomad4 FIN exome
AF:
0.0923
Gnomad4 NFE exome
AF:
0.161
Gnomad4 OTH exome
AF:
0.150
GnomAD4 genome
AF:
0.167
AC:
25499
AN:
152254
Hom.:
2612
Cov.:
32
AF XY:
0.170
AC XY:
12672
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.0699
Gnomad4 AMR
AF:
0.210
Gnomad4 ASJ
AF:
0.304
Gnomad4 EAS
AF:
0.334
Gnomad4 SAS
AF:
0.288
Gnomad4 FIN
AF:
0.178
Gnomad4 NFE
AF:
0.186
Gnomad4 OTH
AF:
0.211
Alfa
AF:
0.181
Hom.:
437
Bravo
AF:
0.166
Asia WGS
AF:
0.366
AC:
1270
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.21
DANN
Benign
0.79

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12621608; hg19: chr2-65300752; API