Variant chr16-722600-A-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.*78T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 452,910 control chromosomes in the GnomAD database, including 249 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 21 hom., cov: 30)

Exomes 𝑓: 0.032 ( 228 hom. )

Consequence

CCDC78
NM_001378030.1 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.188

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:

ANTKMT (HGNC:14152): (adenine nucleotide translocase lysine methyltransferase) Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine trimethylation. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ANTKMT 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=-0.87).

BP6

Variant 16-722600-A-C is Benign according to our data. Variant chr16-722600-A-C is described in ClinVar as [Benign]. Clinvar id is 1287808.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0766 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.*78T>G		3_prime_UTR_variant	14/14	ENST00000345165.10
ANTKMT	NM_023933.3 linkuse as main transcript			downstream_gene_variant		ENST00000569529.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC78	ENST00000345165.10 linkuse as main transcript	c.*78T>G		3_prime_UTR_variant	14/14	5	NM_001378030.1	A2
ANTKMT	ENST00000569529.6 linkuse as main transcript			downstream_gene_variant		1	NM_023933.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0118

AC:

1280

AN:

108676

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0163

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0225

Gnomad ASJ

AF:

0.00479

Gnomad EAS

AF:

0.0113

Gnomad SAS

AF:

0.0839

Gnomad FIN

AF:

0.00340

Gnomad MID

AF:

0.0179

Gnomad NFE

AF:

0.00481

Gnomad OTH

AF:

0.0218

GnomAD3 exomes

AF:

0.0120

AC:

2704

AN:

226136

Hom.:

AF XY:

0.0144

AC XY:

1799

AN XY:

125260

show subpopulations

Gnomad AFR exome

AF:

0.0116

Gnomad AMR exome

AF:

0.00268

Gnomad ASJ exome

AF:

0.00725

Gnomad EAS exome

AF:

0.00481

Gnomad SAS exome

AF:

0.0595

Gnomad FIN exome

AF:

0.00169

Gnomad NFE exome

AF:

0.00440

Gnomad OTH exome

AF:

0.0110

GnomAD4 exome

AF:

0.0323

AC:

11128

AN:

344206

Hom.:

228

Cov.:

AF XY:

0.0350

AC XY:

6669

AN XY:

190762

show subpopulations

Gnomad4 AFR exome

AF:

0.0412

Gnomad4 AMR exome

AF:

0.00444

Gnomad4 ASJ exome

AF:

0.0167

Gnomad4 EAS exome

AF:

0.0574

Gnomad4 SAS exome

AF:

0.0758

Gnomad4 FIN exome

AF:

0.00386

Gnomad4 NFE exome

AF:

0.0228

Gnomad4 OTH exome

AF:

0.0359

GnomAD4 genome

AF:

0.0118

AC:

1287

AN:

108704

Hom.:

Cov.:

AF XY:

0.0140

AC XY:

690

AN XY:

49306

show subpopulations

Gnomad4 AFR

AF:

0.0163

Gnomad4 AMR

AF:

0.0225

Gnomad4 ASJ

AF:

0.00479

Gnomad4 EAS

AF:

0.0113

Gnomad4 SAS

AF:

0.0847

Gnomad4 FIN

AF:

0.00340

Gnomad4 NFE

AF:

0.00481

Gnomad4 OTH

AF:

0.0231

Alfa

AF:

0.00303

Hom.:

Bravo

AF:

0.00816

Asia WGS

AF:

0.0400

AC:

140

AN:

3478

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.9

DANN

Benign

0.49

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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