rs6590113

Positions:

• chr11-124992618-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_025004.3(CCDC15):​c.2070A>G​(p.Glu690=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 1,594,302 control chromosomes in the GnomAD database, including 39,007 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 0.27 (6412 hom., cov: 32)
  • Exomes 𝑓: 0.20 (32595 hom.)
• Consequence: CCDC15 NM_025004.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

Genes affected

CCDC15 (HGNC:25798): (coiled-coil domain containing 15) Located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP7: Synonymous conserved (PhyloP=0.026 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC15	NM_025004.3	c.2070A>G	p.Glu690=	synonymous_variant	10/16	ENST00000344762.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC15	ENST00000344762.6	c.2070A>G	p.Glu690=	synonymous_variant	10/16	5	NM_025004.3	A2
CCDC15	ENST00000529051.5	c.2070A>G	p.Glu690=	synonymous_variant	10/16	5		P4

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40518 AN: 151960 Hom.: 6399 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.266

GnomAD3 exomes AF: 0.220 AC: 50364 AN: 229112 Hom.: 6092 AF XY: 0.219 AC XY: 26987 AN XY: 123314

Gnomad AFR exome AF: 0.447

Gnomad AMR exome AF: 0.181

Gnomad ASJ exome AF: 0.305

Gnomad EAS exome AF: 0.195

Gnomad SAS exome AF: 0.265

Gnomad FIN exome AF: 0.172

Gnomad NFE exome AF: 0.195

Gnomad OTH exome AF: 0.221

GnomAD4 exome AF: 0.204 AC: 294662 AN: 1442224 Hom.: 32595 Cov.: 30 AF XY: 0.206 AC XY: 147182 AN XY: 716082

Gnomad4 AFR exome AF: 0.451

Gnomad4 AMR exome AF: 0.184

Gnomad4 ASJ exome AF: 0.313

Gnomad4 EAS exome AF: 0.200

Gnomad4 SAS exome AF: 0.262

Gnomad4 FIN exome AF: 0.175

Gnomad4 NFE exome AF: 0.191

Gnomad4 OTH exome AF: 0.224

GnomAD4 genome AF: 0.267 AC: 40559 AN: 152078 Hom.: 6412 Cov.: 32 AF XY: 0.263 AC XY: 19553 AN XY: 74344

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.263

Alfa AF: 0.224 Hom.: 1814

Bravo AF: 0.278

Asia WGS AF: 0.244 AC: 849 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6590113; hg19: chr11-124862514; COSMIC: COSV61081853;