3-42766579-C-T

Variant names:

• chr3-42766579-C-T
• rs339665
• NM_144719.4:c.-7+6597G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC13	NM_144719.4	c.-7+6597G>A		intron_variant	Intron 1 of 15	ENST00000310232.11	NP_653320.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC13	ENST00000310232.11	c.-7+6597G>A		intron_variant	Intron 1 of 15	1	NM_144719.4	ENSP00000309836.6
ENSG00000280571	ENST00000648550.1	c.64-8228G>A		intron_variant	Intron 2 of 16			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

African (AFR) AF: 0.991 AC: 39714 AN: 40070

American (AMR) AF: 0.974 AC: 14597 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3329 AN: 3458

East Asian (EAS) AF: 0.999 AC: 5031 AN: 5034

South Asian (SAS) AF: 0.958 AC: 4460 AN: 4654

European-Finnish (FIN) AF: 0.941 AC: 8975 AN: 9534

Middle Eastern (MID) AF: 0.965 AC: 276 AN: 286

European-Non Finnish (NFE) AF: 0.952 AC: 64151 AN: 67420

Other (OTH) AF: 0.971 AC: 1995 AN: 2054

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
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs339665; hg19: chr3-42808071;