rs6766344

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 ENST00000463996.1(CCDC14):​n.66-11326A>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 ENST00000463996.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000463996.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC14	ENST00000479903.5	TSL:5	c.666-11326A>T		intron	N/A	ENSP00000420768.1	H7C5T3
	CCDC14	ENST00000463996.1	TSL:2	n.66-11326A>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6766344;

hg19: chr3-123627786;