chr3-123889564-C-A

Position:

• chr3-123889564-C-A

Variant summary

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

The XM_011513081.3(CCDC14):​c.1882-2100G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,268 control chromosomes in the GnomAD database, including 2,497 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 0.14 (2497 hom., cov: 33)
• Consequence: CCDC14 XM_011513081.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18

Genes affected

CCDC14 (HGNC:25766): (coiled-coil domain containing 14) Involved in protein localization to centrosome. Located in centriolar satellite. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC14	XM_011513081.3	c.1882-2100G>T		intron_variant			XP_011511383.2
		n.123889564C>A		intergenic_region
CCDC14	XR_007095720.1	n.13627-2100G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20921 AN: 152150 Hom.: 2494 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0402

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.138 AC: 20954 AN: 152268 Hom.: 2497 Cov.: 33 AF XY: 0.142 AC XY: 10537 AN XY: 74454

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0402

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0921 Hom.: 170

Bravo AF: 0.146

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.38
DANN	Benign	0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2700380; hg19: chr3-123608411;