chr16-725955-C-A

Variant names:

• chr16-725955-C-A
• rs12448312
• NM_001378030.1:c.180+11G>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001378030.1(CCDC78):​c.180+11G>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 1,559,720 control chromosomes in the GnomAD database, including 45,994 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.20 (3374 hom., cov: 33)
  • Exomes 𝑓: 0.24 (42620 hom.)
• Consequence: CCDC78 NM_001378030.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 1.27
• Publications: 4 publications found

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 Gene-Disease associations (from GenCC):

• congenital myopathy with internal nuclei and atypical cores

  Inheritance: AD Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
• centronuclear myopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 16-725955-C-A is Benign according to our data. Variant chr16-725955-C-A is described in ClinVar as Benign. ClinVar VariationId is 257163.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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378030.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC78	NM_001378030.1	MANE Select	c.180+11G>T		intron	N/A	NP_001364959.1	H3BLT8
	CCDC78	NM_001031737.3		c.180+11G>T		intron	N/A	NP_001026907.2	A2IDD5-1
	CCDC78	NM_001378031.1		c.180+11G>T		intron	N/A	NP_001364960.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC78	ENST00000345165.10	TSL:5 MANE Select	c.180+11G>T		intron	N/A	ENSP00000316851.5	H3BLT8
	CCDC78	ENST00000293889.10	TSL:1	c.180+11G>T		intron	N/A	ENSP00000293889.6	A2IDD5-1
	CCDC78	ENST00000947033.1		c.180+11G>T		intron	N/A	ENSP00000617092.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30061 AN: 151908 Hom.: 3368 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

GnomAD2 exomes AF: 0.211 AC: 35462 AN: 168318 AF XY: 0.222

Gnomad AFR exome AF: 0.127

Gnomad AMR exome AF: 0.108

Gnomad ASJ exome AF: 0.174

Gnomad EAS exome AF: 0.00827

Gnomad FIN exome AF: 0.265

Gnomad NFE exome AF: 0.252

Gnomad OTH exome AF: 0.210

GnomAD4 exome AF: 0.239 AC: 336401 AN: 1407694 Hom.: 42620 Cov.: 38 AF XY: 0.242 AC XY: 168384 AN XY: 695576

African (AFR) AF: 0.122 AC: 3905 AN: 32078

American (AMR) AF: 0.111 AC: 4116 AN: 36970

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 4538 AN: 25340

East Asian (EAS) AF: 0.0222 AC: 817 AN: 36732

South Asian (SAS) AF: 0.320 AC: 25873 AN: 80926

European-Finnish (FIN) AF: 0.265 AC: 12728 AN: 48072

Middle Eastern (MID) AF: 0.154 AC: 879 AN: 5708

European-Non Finnish (NFE) AF: 0.250 AC: 270942 AN: 1083526

Other (OTH) AF: 0.216 AC: 12603 AN: 58342

GnomAD4 genome AF: 0.198 AC: 30092 AN: 152026 Hom.: 3374 Cov.: 33 AF XY: 0.199 AC XY: 14801 AN XY: 74330

African (AFR) AF: 0.127 AC: 5255 AN: 41534

American (AMR) AF: 0.153 AC: 2337 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3468

East Asian (EAS) AF: 0.0129 AC: 67 AN: 5182

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4816

European-Finnish (FIN) AF: 0.258 AC: 2733 AN: 10586

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16850 AN: 67848

Other (OTH) AF: 0.184 AC: 387 AN: 2108

Alfa AF: 0.176 Hom.: 554

Bravo AF: 0.181

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	Congenital myopathy with internal nuclei and atypical cores (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.2
DANN	Benign	0.70
PhyloP100		1.3
PromoterAI		-0.0013	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12448312; hg19: chr16-775955; COSMIC: COSV52402268; COSMIC: COSV52402268;