3-42766579-C-T

Position:

• chr3-42766579-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144719.4(CCDC13):​c.-7+6597G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.966 in 148,410 control chromosomes in the GnomAD database, including 69,257 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.97 (69257 hom., cov: 22)
• Consequence: CCDC13 NM_144719.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

Genes affected

CCDC13 (HGNC:26358): (coiled-coil domain containing 13) Involved in cellular response to DNA damage stimulus; cytoplasmic microtubule organization; and non-motile cilium assembly. Located in centriolar satellite; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000280571 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC13	NM_144719.4	c.-7+6597G>A		intron_variant		ENST00000310232.11	NP_653320.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC13	ENST00000310232.11	c.-7+6597G>A		intron_variant		1	NM_144719.4	ENSP00000309836.6
ENSG00000280571	ENST00000648550.1	c.64-8228G>A		intron_variant				ENSP00000496982.1

Frequencies

GnomAD3 genomes AF: 0.966 AC: 143289 AN: 148342 Hom.: 69219 Cov.: 22

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.961

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.971

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

GnomAD4 genome AF: 0.966 AC: 143361 AN: 148410 Hom.: 69257 Cov.: 22 AF XY: 0.965 AC XY: 69577 AN XY: 72114

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.974

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.958

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.952

Gnomad4 OTH AF: 0.971

Alfa AF: 0.943 Hom.: 2145

Bravo AF: 0.970

Asia WGS AF: 0.986 AC: 3422 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.26

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: rs339665; hg19: chr3-42808071;