Variant chr13-102730310-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001146197.3(CCDC168):c.20387T>C(p.Val6796Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0075 in 1,551,386 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0077 ( 58 hom. )

Consequence

CCDC168
NM_001146197.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.75

Variant links:

Genes affected

CCDC168 (HGNC:26851): (coiled-coil domain containing 168)

CCDC168 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0034114122).

BP6

Variant 13-102730310-A-G is Benign according to our data. Variant chr13-102730310-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2643903.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 58 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC168	NM_001146197.3 linkuse as main transcript	c.20387T>C	p.Val6796Ala	missense_variant	4/4	ENST00000322527.4
CCDC168	XM_011521106.2 linkuse as main transcript	c.20267T>C	p.Val6756Ala	missense_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC168	ENST00000322527.4 linkuse as main transcript	c.20387T>C	p.Val6796Ala	missense_variant	4/4	3	NM_001146197.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00537

AC:

817

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00773

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00885

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00448

AC:

696

AN:

155290

Hom.:

AF XY:

0.00432

AC XY:

355

AN XY:

82240

show subpopulations

Gnomad AFR exome

AF:

0.00126

Gnomad AMR exome

AF:

0.00405

Gnomad ASJ exome

AF:

0.00567

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000264

Gnomad FIN exome

AF:

0.000360

Gnomad NFE exome

AF:

0.00852

Gnomad OTH exome

AF:

0.00435

GnomAD4 exome

AF:

0.00773

AC:

10816

AN:

1399086

Hom.:

Cov.:

AF XY:

0.00753

AC XY:

5194

AN XY:

690052

show subpopulations

Gnomad4 AFR exome

AF:

0.00152

Gnomad4 AMR exome

AF:

0.00417

Gnomad4 ASJ exome

AF:

0.00548

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000240

Gnomad4 FIN exome

AF:

0.000611

Gnomad4 NFE exome

AF:

0.00930

Gnomad4 OTH exome

AF:

0.00662

GnomAD4 genome

AF:

0.00536

AC:

816

AN:

152300

Hom.:

Cov.:

AF XY:

0.00493

AC XY:

367

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00140

Gnomad4 AMR

AF:

0.00772

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00883

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00768

Hom.:

Bravo

AF:

0.00610

TwinsUK

AF:

0.0102

AC:

ALSPAC

AF:

0.00908

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00849

AC:

ExAC

AF:

0.00324

AC:

Asia WGS

AF:

0.000867

AC:

AN:

3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

CCDC168: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Uncertain

0.99

Eigen

Benign

-0.63

Eigen_PC

Benign

-0.55

FATHMM_MKL

Benign

0.045

M_CAP

Benign

0.012

MetaRNN

Benign

0.0034

MetaSVM

Benign

-0.97

MutationTaster

Benign

1.0

PrimateAI

Benign

0.28

REVEL

Benign

0.038

Sift4G

Uncertain

0.0060

Vest4

0.14

MVP

0.040

ClinPred

0.013

GERP RS

2.7

gMVP

0.031

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over