Variant rs10783231 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001013635.4(CCDC184):c.420A>C(p.Glu140Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,553,894 control chromosomes in the GnomAD database, including 429,862 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.70 ( 37679 hom., cov: 29)

Exomes 𝑓: 0.74 ( 392183 hom. )

Consequence

CCDC184
NM_001013635.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

Variant links:

Genes affected

CCDC184 (HGNC:33749): (coiled-coil domain containing 184) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CCDC184 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.957121E-7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC184	NM_001013635.4 linkuse as main transcript	c.420A>C	p.Glu140Asp	missense_variant	1/1	ENST00000316554.5	NP_001013657.3	Q52MB2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC184	ENST00000316554.5 linkuse as main transcript	c.420A>C	p.Glu140Asp	missense_variant	1/1	6	NM_001013635.4	ENSP00000320849.3		Q52MB2

Frequencies

GnomAD3 genomes

AF:

0.698

AC:

105940

AN:

151700

Hom.:

37649

Cov.:

show subpopulations

Gnomad AFR

AF:

0.643

Gnomad AMI

AF:

0.784

Gnomad AMR

AF:

0.595

Gnomad ASJ

AF:

0.811

Gnomad EAS

AF:

0.406

Gnomad SAS

AF:

0.653

Gnomad FIN

AF:

0.715

Gnomad MID

AF:

0.845

Gnomad NFE

AF:

0.770

Gnomad OTH

AF:

0.722

GnomAD3 exomes

AF:

0.669

AC:

105186

AN:

157124

Hom.:

36689

AF XY:

0.681

AC XY:

58249

AN XY:

85578

show subpopulations

Gnomad AFR exome

AF:

0.645

Gnomad AMR exome

AF:

0.469

Gnomad ASJ exome

AF:

0.800

Gnomad EAS exome

AF:

0.415

Gnomad SAS exome

AF:

0.676

Gnomad FIN exome

AF:

0.701

Gnomad NFE exome

AF:

0.772

Gnomad OTH exome

AF:

0.718

GnomAD4 exome

AF:

0.743

AC:

1041905

AN:

1402076

Hom.:

392183

Cov.:

AF XY:

0.743

AC XY:

514812

AN XY:

693110

show subpopulations

Gnomad4 AFR exome

AF:

0.643

Gnomad4 AMR exome

AF:

0.486

Gnomad4 ASJ exome

AF:

0.801

Gnomad4 EAS exome

AF:

0.415

Gnomad4 SAS exome

AF:

0.676

Gnomad4 FIN exome

AF:

0.709

Gnomad4 NFE exome

AF:

0.771

Gnomad4 OTH exome

AF:

0.726

GnomAD4 genome

AF:

0.698

AC:

106015

AN:

151818

Hom.:

37679

Cov.:

AF XY:

0.692

AC XY:

51309

AN XY:

74156

show subpopulations

Gnomad4 AFR

AF:

0.643

Gnomad4 AMR

AF:

0.595

Gnomad4 ASJ

AF:

0.811

Gnomad4 EAS

AF:

0.407

Gnomad4 SAS

AF:

0.653

Gnomad4 FIN

AF:

0.715

Gnomad4 NFE

AF:

0.770

Gnomad4 OTH

AF:

0.717

Alfa

AF:

0.752

Hom.:

67995

Bravo

AF:

0.686

TwinsUK

AF:

0.770

AC:

2854

ALSPAC

AF:

0.761

AC:

2931

ESP6500AA

AF:

0.668

AC:

2887

ESP6500EA

AF:

0.785

AC:

6639

ExAC

AF:

0.626

AC:

68884

Asia WGS

AF:

0.537

AC:

1871

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.052

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.3

DANN

Benign

0.54

DEOGEN2

Benign

0.0023

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0037

LIST_S2

Benign

0.17

MetaRNN

Benign

9.0e-7

MetaSVM

Benign

-0.96

MutationAssessor

Benign

-0.34

PROVEAN

Benign

0.80

REVEL

Benign

0.032

Sift

Benign

1.0

Sift4G

Benign

0.56

Polyphen

0.0

Vest4

0.033

MutPred

0.084

Loss of helix (P = 0.0444);

MPC

0.34

ClinPred

0.0012

GERP RS

-1.7

Varity_R

0.049

gMVP

0.024

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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