rs2222823

Variant names:

• chr3-123885940-T-A
• rs2222823
• XR_007095720.1:n.13826-155A>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.13826-155A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 151,948 control chromosomes in the GnomAD database, including 2,449 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 (2449 hom., cov: 31)
• Consequence: CCDC14 XR_007095720.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC14	XR_007095720.1	n.13826-155A>T		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20792 AN: 151830 Hom.: 2446 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0407

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.137 AC: 20825 AN: 151948 Hom.: 2449 Cov.: 31 AF XY: 0.141 AC XY: 10466 AN XY: 74280

African (AFR) AF: 0.295 AC: 12218 AN: 41370

American (AMR) AF: 0.107 AC: 1638 AN: 15280

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

East Asian (EAS) AF: 0.360 AC: 1850 AN: 5142

South Asian (SAS) AF: 0.150 AC: 721 AN: 4806

European-Finnish (FIN) AF: 0.111 AC: 1173 AN: 10560

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0407 AC: 2765 AN: 68000

Other (OTH) AF: 0.124 AC: 263 AN: 2116

Alfa AF: 0.0924 Hom.: 169

Bravo AF: 0.146

Asia WGS AF: 0.260 AC: 902 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.013
DANN	Benign	0.16
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2222823; hg19: chr3-123604787;