rs6741255

Variant summary

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

The NM_015147.3(CEP68):​c.2104+1807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,156 control chromosomes in the GnomAD database, including 32,737 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 0.65 ( 32737 hom., cov: 33)

Consequence

CEP68
NM_015147.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.832
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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CEP68NM_015147.3 linkuse as main transcriptc.2104+1807C>T intron_variant ENST00000377990.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CEP68ENST00000377990.7 linkuse as main transcriptc.2104+1807C>T intron_variant 1 NM_015147.3 P2Q76N32-1

Frequencies

GnomAD3 genomes
AF:
0.653
AC:
99343
AN:
152038
Hom.:
32723
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.586
Gnomad AMI
AF:
0.747
Gnomad AMR
AF:
0.670
Gnomad ASJ
AF:
0.566
Gnomad EAS
AF:
0.663
Gnomad SAS
AF:
0.616
Gnomad FIN
AF:
0.714
Gnomad MID
AF:
0.576
Gnomad NFE
AF:
0.688
Gnomad OTH
AF:
0.626
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.653
AC:
99392
AN:
152156
Hom.:
32737
Cov.:
33
AF XY:
0.654
AC XY:
48643
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.585
Gnomad4 AMR
AF:
0.671
Gnomad4 ASJ
AF:
0.566
Gnomad4 EAS
AF:
0.664
Gnomad4 SAS
AF:
0.615
Gnomad4 FIN
AF:
0.714
Gnomad4 NFE
AF:
0.688
Gnomad4 OTH
AF:
0.621
Alfa
AF:
0.669
Hom.:
4213
Bravo
AF:
0.648
Asia WGS
AF:
0.566
AC:
1972
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.078
DANN
Benign
0.43

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: rs6741255; hg19: chr2-65306905; API