chr10-114135200-C-T

Variant names:

• chr10-114135200-C-T
• rs7902873
• NM_018017.4:c.1513-145G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_018017.4(CCDC186):​c.1513-145G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000016 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCDC186 NM_018017.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 3 publications found

Genes affected

CCDC186 (HGNC:24349): (coiled-coil domain containing 186) Predicted to enable small GTPase binding activity. Predicted to be involved in vesicle cytoskeletal trafficking. Predicted to act upstream of or within insulin secretion involved in cellular response to glucose stimulus and response to bacterium. Predicted to be located in Golgi apparatus. Predicted to be active in trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018017.4. 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
	CCDC186	NM_018017.4	MANE Select	c.1513-145G>A		intron	N/A	NP_060487.2
	CCDC186	NM_001321829.1		c.1513-145G>A		intron	N/A	NP_001308758.1
	CCDC186	NR_135815.1		n.1905-145G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC186	ENST00000369287.8	TSL:1 MANE Select	c.1513-145G>A		intron	N/A	ENSP00000358293.3
	CCDC186	ENST00000648613.1		c.1513-145G>A		intron	N/A	ENSP00000498136.1
	CCDC186	ENST00000912199.1		c.1408-145G>A		intron	N/A	ENSP00000582258.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 151896 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000157 AC: 1 AN: 635838 Hom.: 0 AF XY: 0.00000312 AC XY: 1 AN XY: 320018

African (AFR) AF: 0.00 AC: 0 AN: 12932

American (AMR) AF: 0.00 AC: 0 AN: 8994

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13094

East Asian (EAS) AF: 0.00 AC: 0 AN: 24184

South Asian (SAS) AF: 0.0000311 AC: 1 AN: 32146

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26938

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2230

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 484572

Other (OTH) AF: 0.00 AC: 0 AN: 30748

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 151896 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 74172

African (AFR) AF: 0.00 AC: 0 AN: 41390

American (AMR) AF: 0.00 AC: 0 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10526

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67938

Other (OTH) AF: 0.00 AC: 0 AN: 2090

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.72
DANN	Benign	0.94
PhyloP100		-0.47

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

Other links and lift over

dbSNP: rs7902873; hg19: chr10-115894959;