2-130341809-G-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_032357.4(CCDC115):c.215+32C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.23 (0 hom., cov: 0)
  • Exomes 𝑓: 0.24 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCDC115 NM_032357.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.54

Genes affected

CCDC115 (HGNC:28178): (coiled-coil domain containing 115) The protein encoded by this gene has been observed to localize to the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC) and coat protein complex I (COPI) vesicles in some human cells. The encoded protein shares some homology with the yeast V-ATPase assembly factor Vma22p, and the orthologous protein in mouse promotes cell proliferation and suppresses cell death. Defects in this gene are a cause of congenital disorder of glycosylation, type IIo in humans. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 2-130341809-G-C is Benign according to our data. Variant chr2-130341809-G-C is described in ClinVar as [Benign]. Clinvar id is 1242374.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC115	NM_032357.4	c.215+32C>G		intron_variant		ENST00000259229.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC115	ENST00000259229.7	c.215+32C>G		intron_variant		1	NM_032357.4	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 6967 AN: 30308 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.0714

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.258

GnomAD3 exomes AF: 0.259 AC: 13954 AN: 53782 Hom.: 0 AF XY: 0.254 AC XY: 7539 AN XY: 29646

Gnomad AFR exome AF: 0.276

Gnomad AMR exome AF: 0.395

Gnomad ASJ exome AF: 0.211

Gnomad EAS exome AF: 0.294

Gnomad SAS exome AF: 0.305

Gnomad FIN exome AF: 0.168

Gnomad NFE exome AF: 0.216

Gnomad OTH exome AF: 0.323

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.241 AC: 77368 AN: 321222 Hom.: 0 Cov.: 8 AF XY: 0.251 AC XY: 42439 AN XY: 168880

Gnomad4 AFR exome AF: 0.188

Gnomad4 AMR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.244

Gnomad4 EAS exome AF: 0.169

Gnomad4 SAS exome AF: 0.424

Gnomad4 FIN exome AF: 0.196

Gnomad4 NFE exome AF: 0.206

Gnomad4 OTH exome AF: 0.246

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.230 AC: 6968 AN: 30334 Hom.: 0 Cov.: 0 AF XY: 0.213 AC XY: 3284 AN XY: 15434

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.256

Alfa AF: 0.0000727 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 07, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.4
Dann	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs755618222; hg19: chr2-131099382;