Variant 1-32204044-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_024296.5(CCDC28B):c.330C>T(p.Phe110=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0128 in 1,554,330 control chromosomes in the GnomAD database, including 236 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance,risk factor (no stars).

Frequency

Genomes: 𝑓 0.010 ( 25 hom., cov: 32)

Exomes 𝑓: 0.013 ( 211 hom. )

Consequence

CCDC28B
NM_024296.5 splice_region, synonymous

Scores

Splicing: ADA: 0.004443

Clinical Significance

Uncertain significance; risk factor no assertion criteria provided U:1O:1

Conservation

PhyloP100: -1.46

Variant links:

Genes affected

CCDC28B (HGNC:28163): (coiled-coil domain containing 28B) The product of this gene localizes to centrosomes and basal bodies. The protein colocalizes with several proteins associated with Bardet-Biedl syndrome (BBS) and participates in the regulation of cilia development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

CCDC28B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP7

Synonymous conserved (PhyloP=-1.46 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC28B	NM_024296.5 linkuse as main transcript	c.330C>T	p.Phe110=	splice_region_variant, synonymous_variant	3/6	ENST00000373602.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC28B	ENST00000373602.10 linkuse as main transcript	c.330C>T	p.Phe110=	splice_region_variant, synonymous_variant	3/6	1	NM_024296.5	P1	Q9BUN5-1

Frequencies

GnomAD3 genomes

AF:

0.0105

AC:

1591

AN:

152106

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00290

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0143

Gnomad ASJ

AF:

0.0645

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00684

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0136

Gnomad OTH

AF:

0.0172

GnomAD3 exomes

AF:

0.0116

AC:

2358

AN:

203610

Hom.:

AF XY:

0.0122

AC XY:

1322

AN XY:

108128

show subpopulations

Gnomad AFR exome

AF:

0.00218

Gnomad AMR exome

AF:

0.00883

Gnomad ASJ exome

AF:

0.0689

Gnomad EAS exome

AF:

0.0000587

Gnomad SAS exome

AF:

0.0104

Gnomad FIN exome

AF:

0.000908

Gnomad NFE exome

AF:

0.0145

Gnomad OTH exome

AF:

0.0202

GnomAD4 exome

AF:

0.0131

AC:

18358

AN:

1402106

Hom.:

211

Cov.:

AF XY:

0.0132

AC XY:

9120

AN XY:

691058

show subpopulations

Gnomad4 AFR exome

AF:

0.00449

Gnomad4 AMR exome

AF:

0.00931

Gnomad4 ASJ exome

AF:

0.0676

Gnomad4 EAS exome

AF:

0.0000256

Gnomad4 SAS exome

AF:

0.0108

Gnomad4 FIN exome

AF:

0.00113

Gnomad4 NFE exome

AF:

0.0131

Gnomad4 OTH exome

AF:

0.0172

GnomAD4 genome

AF:

0.0105

AC:

1591

AN:

152224

Hom.:

Cov.:

AF XY:

0.00978

AC XY:

728

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00289

Gnomad4 AMR

AF:

0.0143

Gnomad4 ASJ

AF:

0.0645

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00705

Gnomad4 FIN

AF:

0.00113

Gnomad4 NFE

AF:

0.0136

Gnomad4 OTH

AF:

0.0175

Alfa

AF:

0.0161

Hom.:

Bravo

AF:

0.0112

Asia WGS

AF:

0.00462

AC:

AN:

3478

ClinVar

Significance: Uncertain significance; risk factor

Submissions summary: Uncertain:1Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Bardet-Biedl syndrome

Uncertain:1

Uncertain significance, no assertion criteria provided

research

Tolun Lab, Human Genetics Laboratory, Bogazici University

- -

Bardet-Biedl syndrome 1, modifier of

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jan 19, 2006

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

4.6

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0044

dbscSNV1_RF

Benign

0.65

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.

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