chr3-123908939-T-A

Variant names:

• chr3-123908939-T-A
• rs6766344
• ENST00000479903.5:c.666-11326A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000479903.5(CCDC14):​c.666-11326A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0349 in 152,294 control chromosomes in the GnomAD database, including 118 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 0.035 (118 hom., cov: 32)
• Consequence: CCDC14 ENST00000479903.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC14	XM_005247715.5	c.1779-11326A>T		intron_variant	Intron 12 of 12		XP_005247772.2
CCDC14	XM_011513081.3	c.1779-11326A>T		intron_variant	Intron 12 of 13		XP_011511383.2
CCDC14	XM_047448748.1	c.1656-11326A>T		intron_variant	Intron 11 of 11		XP_047304704.1
CCDC14	XR_007095720.1	n.13524-11326A>T		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC14	ENST00000479903.5	c.666-11326A>T		intron_variant	Intron 5 of 5	5		ENSP00000420768.1
CCDC14	ENST00000463996.1	n.66-11326A>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0349 AC: 5304 AN: 152176 Hom.: 118 Cov.: 32

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.0466

Gnomad FIN AF: 0.0122

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0349 AC: 5310 AN: 152294 Hom.: 118 Cov.: 32 AF XY: 0.0332 AC XY: 2470 AN XY: 74478

African (AFR) AF: 0.0108 AC: 448 AN: 41556

American (AMR) AF: 0.0307 AC: 469 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3470

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5176

South Asian (SAS) AF: 0.0472 AC: 228 AN: 4826

European-Finnish (FIN) AF: 0.0122 AC: 130 AN: 10624

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0529 AC: 3598 AN: 68024

Other (OTH) AF: 0.0450 AC: 95 AN: 2112

Alfa AF: 0.0386 Hom.: 16

Bravo AF: 0.0347

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.3
DANN	Benign	0.61
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs6766344; hg19: chr3-123627786;