Variant 16-722842-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001378030.1(CCDC78):c.1302-53A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 1,608,772 control chromosomes in the GnomAD database, including 220,565 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 24510 hom., cov: 34)

Exomes 𝑓: 0.51 ( 196055 hom. )

Consequence

CCDC78
NM_001378030.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.420

Variant links:

Genes affected

CCDC78 (HGNC:14153): (coiled-coil domain containing 78) Involved in de novo centriole assembly involved in multi-ciliated epithelial cell differentiation and skeletal muscle contraction. Located in several cellular components, including centriole; deuterosome; and sarcolemma. Implicated in centronuclear myopathy 4. [provided by Alliance of Genome Resources, Apr 2022]

CCDC78 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 16-722842-T-C is Benign according to our data. Variant chr16-722842-T-C is described in ClinVar as [Benign]. Clinvar id is 1185523.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC78	NM_001378030.1 linkuse as main transcript	c.1302-53A>G		intron_variant		ENST00000345165.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC78	ENST00000345165.10 linkuse as main transcript	c.1302-53A>G		intron_variant		5	NM_001378030.1	A2

Frequencies

GnomAD3 genomes

AF:

0.557

AC:

84623

AN:

152008

Hom.:

24473

Cov.:

show subpopulations

Gnomad AFR

AF:

0.635

Gnomad AMI

AF:

0.456

Gnomad AMR

AF:

0.602

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.809

Gnomad SAS

AF:

0.766

Gnomad FIN

AF:

0.607

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.469

Gnomad OTH

AF:

0.489

GnomAD3 exomes

AF:

0.586

AC:

145688

AN:

248656

Hom.:

45280

AF XY:

0.582

AC XY:

78533

AN XY:

135024

show subpopulations

Gnomad AFR exome

AF:

0.646

Gnomad AMR exome

AF:

0.726

Gnomad ASJ exome

AF:

0.397

Gnomad EAS exome

AF:

0.816

Gnomad SAS exome

AF:

0.763

Gnomad FIN exome

AF:

0.607

Gnomad NFE exome

AF:

0.465

Gnomad OTH exome

AF:

0.509

GnomAD4 exome

AF:

0.507

AC:

739101

AN:

1456646

Hom.:

196055

Cov.:

AF XY:

0.513

AC XY:

371591

AN XY:

724512

show subpopulations

Gnomad4 AFR exome

AF:

0.636

Gnomad4 AMR exome

AF:

0.709

Gnomad4 ASJ exome

AF:

0.399

Gnomad4 EAS exome

AF:

0.800

Gnomad4 SAS exome

AF:

0.756

Gnomad4 FIN exome

AF:

0.608

Gnomad4 NFE exome

AF:

0.464

Gnomad4 OTH exome

AF:

0.510

GnomAD4 genome

AF:

0.557

AC:

84714

AN:

152126

Hom.:

24510

Cov.:

AF XY:

0.569

AC XY:

42307

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.635

Gnomad4 AMR

AF:

0.603

Gnomad4 ASJ

AF:

0.398

Gnomad4 EAS

AF:

0.809

Gnomad4 SAS

AF:

0.767

Gnomad4 FIN

AF:

0.607

Gnomad4 NFE

AF:

0.469

Gnomad4 OTH

AF:

0.493

Alfa

AF:

0.480

Hom.:

23039

Bravo

AF:

0.555

Asia WGS

AF:

0.760

AC:

2638

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 06, 2018	- -

Congenital myopathy with internal nuclei and atypical cores

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.6

DANN

Benign

0.47

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.

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