chr17-44900676-C-A

Position:

• chr17-44900676-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_213607.3(CCDC103):​c.-9-314C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 152,010 control chromosomes in the GnomAD database, including 34,512 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.67 (34512 hom., cov: 32)
• Consequence: CCDC103 NM_213607.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.72

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 17-44900676-C-A is Benign according to our data. Variant chr17-44900676-C-A is described in ClinVar as [Benign]. Clinvar id is 1178677.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC103	NM_213607.3	c.-9-314C>A		intron_variant		ENST00000417826.3	NP_998772.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC103	ENST00000417826.3	c.-9-314C>A		intron_variant		1	NM_213607.3	ENSP00000391692	P1

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101189 AN: 151890 Hom.: 34477 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.645

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.666 AC: 101276 AN: 152010 Hom.: 34512 Cov.: 32 AF XY: 0.659 AC XY: 48940 AN XY: 74262

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.638

Alfa AF: 0.645 Hom.: 6482

Bravo AF: 0.674

Asia WGS AF: 0.603 AC: 2096 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	14
DANN	Benign	0.69

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: rs3809756; hg19: chr17-42978044;