rs2700380

Variant names:

• chr3-123889564-C-A
• rs2700380
• XM_011513081.3:c.1882-2100G>T

Variant summary

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

The XR_007095720.1(CCDC14):​n.13627-2100G>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 XR_007095720.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.297 AC: 12324 AN: 41534

American (AMR) AF: 0.107 AC: 1641 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1875 AN: 5182

South Asian (SAS) AF: 0.151 AC: 728 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1190 AN: 10614

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0402 AC: 2737 AN: 68020

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.101 Hom.: 213

Bravo AF: 0.146

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.38
DANN	Benign	0.14
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs2700380; hg19: chr3-123608411;