rs6590113

Variant names:

• chr11-124992618-A-G
• rs6590113
• NM_025004.3:c.2070A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-124992618-A-G
• chr11-124992618-A-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_025004.3(CCDC15):​c.2070A>G​(p.Glu690Glu) 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
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025004.3. 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
	CCDC15	NM_025004.3	MANE Select	c.2070A>G	p.Glu690Glu	synonymous	Exon 10 of 16	NP_079280.2	Q0P6D6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC15	ENST00000344762.6	TSL:5 MANE Select	c.2070A>G	p.Glu690Glu	synonymous	Exon 10 of 16	ENSP00000341684.5	Q0P6D6
	CCDC15	ENST00000921762.1		c.2190A>G	p.Glu730Glu	synonymous	Exon 11 of 17	ENSP00000591821.1
	CCDC15	ENST00000529051.5	TSL:5	c.2070A>G	p.Glu690Glu	synonymous	Exon 10 of 16	ENSP00000435403.1	E9PKB1

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

GnomAD2 exomes AF: 0.220 AC: 50364 AN: 229112 AF XY: 0.219

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 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

African (AFR) AF: 0.451 AC: 14909 AN: 33022

American (AMR) AF: 0.184 AC: 7896 AN: 42858

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 8045 AN: 25670

East Asian (EAS) AF: 0.200 AC: 7857 AN: 39368

South Asian (SAS) AF: 0.262 AC: 21778 AN: 83088

European-Finnish (FIN) AF: 0.175 AC: 9235 AN: 52666

Middle Eastern (MID) AF: 0.261 AC: 1499 AN: 5742

European-Non Finnish (NFE) AF: 0.191 AC: 210035 AN: 1100068

Other (OTH) AF: 0.224 AC: 13408 AN: 59742

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

African (AFR) AF: 0.442 AC: 18321 AN: 41428

American (AMR) AF: 0.199 AC: 3041 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3472

East Asian (EAS) AF: 0.190 AC: 984 AN: 5184

South Asian (SAS) AF: 0.276 AC: 1331 AN: 4816

European-Finnish (FIN) AF: 0.178 AC: 1884 AN: 10572

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.191 AC: 13000 AN: 68000

Other (OTH) AF: 0.263 AC: 556 AN: 2114

Alfa AF: 0.229 Hom.: 2023

Bravo AF: 0.278

Asia WGS AF: 0.244 AC: 849 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.34
PhyloP100		0.026
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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