Variant chr10-93503133-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_018131.5(CEP55):c.204T>A(p.Ala68=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 1,613,340 control chromosomes in the GnomAD database, including 4,452 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.050 ( 248 hom., cov: 33)

Exomes 𝑓: 0.072 ( 4204 hom. )

Consequence

CEP55
NM_018131.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.721

Variant links:

Genes affected

CEP55 (HGNC:1161): (centrosomal protein 55) Enables identical protein binding activity. Involved in cranial skeletal system development; establishment of protein localization; and midbody abscission. Acts upstream of or within mitotic cytokinesis. Located in Flemming body; centriolar satellite; and plasma membrane. Implicated in multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia and hydranencephaly. [provided by Alliance of Genome Resources, Apr 2022]

CEP55 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 10-93503133-T-A is Benign according to our data. Variant chr10-93503133-T-A is described in ClinVar as [Benign]. Clinvar id is 1561146.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.721 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP55	NM_018131.5 linkuse as main transcript	c.204T>A	p.Ala68=	synonymous_variant	3/9	ENST00000371485.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP55	ENST00000371485.8 linkuse as main transcript	c.204T>A	p.Ala68=	synonymous_variant	3/9	1	NM_018131.5	P1	Q53EZ4-1

Frequencies

GnomAD3 genomes

AF:

0.0497

AC:

7565

AN:

152142

Hom.:

249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0146

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0346

Gnomad ASJ

AF:

0.0455

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0184

Gnomad FIN

AF:

0.0859

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0758

Gnomad OTH

AF:

0.0435

GnomAD3 exomes

AF:

0.0529

AC:

13255

AN:

250668

Hom.:

461

AF XY:

0.0528

AC XY:

7157

AN XY:

135480

show subpopulations

Gnomad AFR exome

AF:

0.0140

Gnomad AMR exome

AF:

0.0280

Gnomad ASJ exome

AF:

0.0433

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0205

Gnomad FIN exome

AF:

0.0902

Gnomad NFE exome

AF:

0.0766

Gnomad OTH exome

AF:

0.0596

GnomAD4 exome

AF:

0.0715

AC:

104498

AN:

1461080

Hom.:

4204

Cov.:

AF XY:

0.0699

AC XY:

50782

AN XY:

726818

show subpopulations

Gnomad4 AFR exome

AF:

0.0111

Gnomad4 AMR exome

AF:

0.0281

Gnomad4 ASJ exome

AF:

0.0428

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0211

Gnomad4 FIN exome

AF:

0.0867

Gnomad4 NFE exome

AF:

0.0821

Gnomad4 OTH exome

AF:

0.0626

GnomAD4 genome

AF:

0.0497

AC:

7562

AN:

152260

Hom.:

248

Cov.:

AF XY:

0.0492

AC XY:

3664

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0146

Gnomad4 AMR

AF:

0.0346

Gnomad4 ASJ

AF:

0.0455

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0180

Gnomad4 FIN

AF:

0.0859

Gnomad4 NFE

AF:

0.0758

Gnomad4 OTH

AF:

0.0430

Alfa

AF:

0.0650

Hom.:

118

Bravo

AF:

0.0453

Asia WGS

AF:

0.00606

AC:

AN:

3478

EpiCase

AF:

0.0718

EpiControl

AF:

0.0711

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 24, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

8.6

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over