dbSNP rs8079610: CCDC103:c.277-63C>A (chr17-44902302-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_213607.3(CCDC103):c.277-63C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,600,552 control chromosomes in the GnomAD database, including 59,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5277 hom., cov: 32)

Exomes 𝑓: 0.27 ( 54313 hom. )

Consequence

CCDC103
NM_213607.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.50

Variant links:

Genes affected

CCDC103 (HGNC:32700): (coiled-coil domain containing 103) Enables protein homodimerization activity. Involved in axonemal dynein complex assembly; cilium movement; and determination of left/right symmetry. Predicted to be located in axoneme. Predicted to be part of outer dynein arm. Implicated in primary ciliary dyskinesia 17. [provided by Alliance of Genome Resources, Apr 2022]

CCDC103 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=-0.89).

BP6

Variant 17-44902302-C-A is Benign according to our data. Variant chr17-44902302-C-A is described in ClinVar as [Benign]. Clinvar id is 402498.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-44902302-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC103	NM_213607.3 link	c.277-63C>A		intron_variant	Intron 3 of 3	ENST00000417826.3	NP_998772.1	Q8IW40-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCDC103	ENST00000417826.3 link	c.277-63C>A	intron_variant	Intron 3 of 3	1	NM_213607.3	ENSP00000391692.2	Q8IW40-1
CCDC103	ENST00000410006.6 link	c.277-63C>A	intron_variant	Intron 3 of 3	2		ENSP00000387252.1	Q8IW40-1
CCDC103	ENST00000357776.6 link	c.277-63C>A	intron_variant	Intron 3 of 3	2		ENSP00000350420.2	F8W6J8
CCDC103	ENST00000410027.5 link	c.277-16C>A	intron_variant	Intron 3 of 3	4		ENSP00000386640.1	Q8IW40-2

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39732

AN:

151988

Hom.:

5272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.252

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.264

GnomAD3 exomes

AF:

0.268

AC:

66716

AN:

248638

Hom.:

9201

AF XY:

0.269

AC XY:

36230

AN XY:

134698

show subpopulations

Gnomad AFR exome

AF:

0.233

Gnomad AMR exome

AF:

0.224

Gnomad ASJ exome

AF:

0.245

Gnomad EAS exome

AF:

0.255

Gnomad SAS exome

AF:

0.283

Gnomad FIN exome

AF:

0.321

Gnomad NFE exome

AF:

0.277

Gnomad OTH exome

AF:

0.268

GnomAD4 exome

AF:

0.273

AC:

395513

AN:

1448446

Hom.:

54313

Cov.:

AF XY:

0.274

AC XY:

197545

AN XY:

721464

show subpopulations

Gnomad4 AFR exome

AF:

0.233

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.238

Gnomad4 EAS exome

AF:

0.218

Gnomad4 SAS exome

AF:

0.283

Gnomad4 FIN exome

AF:

0.316

Gnomad4 NFE exome

AF:

0.277

Gnomad4 OTH exome

AF:

0.264

GnomAD4 genome

AF:

0.261

AC:

39759

AN:

152106

Hom.:

5277

Cov.:

AF XY:

0.261

AC XY:

19405

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.232

Gnomad4 AMR

AF:

0.226

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.252

Gnomad4 SAS

AF:

0.272

Gnomad4 FIN

AF:

0.318

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.262

Alfa

AF:

0.278

Hom.:

1092

Bravo

AF:

0.253

Asia WGS

AF:

0.228

AC:

791

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.066

DANN

Benign

0.28

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