dbSNP rs17091403: CCDC186:c.-193G>A (chr10-114174146-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018017.4(CCDC186):c.-193G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 470,688 control chromosomes in the GnomAD database, including 1,737 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 0.075 ( 514 hom., cov: 33)

Exomes 𝑓: 0.078 ( 1223 hom. )

Consequence

CCDC186
NM_018017.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.161

Variant links:

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]

CCDC186 links:

MIR2110 (HGNC:37071): (microRNA 2110) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR2110 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0997 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC186	NM_018017.4 link	c.-193G>A		5_prime_UTR_variant	Exon 1 of 16	ENST00000369287.8	NP_060487.2	Q7Z3E2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC186	ENST00000369287.8 link	c.-193G>A		5_prime_UTR_variant	Exon 1 of 16	1	NM_018017.4	ENSP00000358293.3		Q7Z3E2

Frequencies

GnomAD3 genomes

AF:

0.0751

AC:

11437

AN:

152220

Hom.:

514

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0501

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.0445

Gnomad ASJ

AF:

0.0409

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0389

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0616

GnomAD3 exomes

AF:

0.0667

AC:

10136

AN:

152078

Hom.:

425

AF XY:

0.0666

AC XY:

5372

AN XY:

80720

show subpopulations

Gnomad AFR exome

AF:

0.0510

Gnomad AMR exome

AF:

0.0346

Gnomad ASJ exome

AF:

0.0400

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0391

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.0977

Gnomad OTH exome

AF:

0.0617

GnomAD4 exome

AF:

0.0779

AC:

24811

AN:

318350

Hom.:

1223

Cov.:

AF XY:

0.0755

AC XY:

13567

AN XY:

179766

show subpopulations

Gnomad4 AFR exome

AF:

0.0518

Gnomad4 AMR exome

AF:

0.0349

Gnomad4 ASJ exome

AF:

0.0400

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0418

Gnomad4 FIN exome

AF:

0.112

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.0724

GnomAD4 genome

AF:

0.0750

AC:

11432

AN:

152338

Hom.:

514

Cov.:

AF XY:

0.0731

AC XY:

5446

AN XY:

74500

show subpopulations

Gnomad4 AFR

AF:

0.0499

Gnomad4 AMR

AF:

0.0444

Gnomad4 ASJ

AF:

0.0409

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0383

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.102

Gnomad4 OTH

AF:

0.0605

Alfa

AF:

0.0881

Hom.:

574

Bravo

AF:

0.0665

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

3.8

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over