rs12448311

chr16-725954-C-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001378030.1(CCDC78):c.180+12G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,560,678 control chromosomes in the GnomAD database, including 46,014 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.20 (3373 hom., cov: 33)
  • Exomes 𝑓: 0.24 (42641 hom.)
• Consequence: CCDC78 NM_001378030.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -1.34

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 16-725954-C-A is Benign according to our data. Variant chr16-725954-C-A is described in ClinVar as [Benign]. Clinvar id is 257164.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC78	NM_001378030.1	c.180+12G>T		intron_variant		ENST00000345165.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC78	ENST00000345165.10	c.180+12G>T		intron_variant		5	NM_001378030.1	A2

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30060 AN: 151908 Hom.: 3367 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.184

GnomAD3 exomes AF: 0.210 AC: 35590 AN: 169314 Hom.: 4368 AF XY: 0.222 AC XY: 20011 AN XY: 90258

Gnomad AFR exome AF: 0.127

Gnomad AMR exome AF: 0.108

Gnomad ASJ exome AF: 0.174

Gnomad EAS exome AF: 0.00819

Gnomad SAS exome AF: 0.320

Gnomad FIN exome AF: 0.265

Gnomad NFE exome AF: 0.251

Gnomad OTH exome AF: 0.210

GnomAD4 exome AF: 0.239 AC: 336507 AN: 1408652 Hom.: 42641 Cov.: 38 AF XY: 0.242 AC XY: 168460 AN XY: 696156

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.111

Gnomad4 ASJ exome AF: 0.179

Gnomad4 EAS exome AF: 0.0222

Gnomad4 SAS exome AF: 0.320

Gnomad4 FIN exome AF: 0.265

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.198 AC: 30091 AN: 152026 Hom.: 3373 Cov.: 33 AF XY: 0.199 AC XY: 14799 AN XY: 74322

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0129

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.184

Alfa AF: 0.231 Hom.: 808

Bravo AF: 0.181

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

-

- -

Congenital myopathy with internal nuclei and atypical cores Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 06, 2023

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.45
Dann	Benign	0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs12448311; hg19: chr16-775954; COSMIC: COSV52402262; COSMIC: COSV52402262;