Variant 2-178834304-C-T 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_173648.4(CCDC141):c.4462G>A(p.Gly1488Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000619 in 1,535,952 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0016 ( 2 hom., cov: 32)

Exomes 𝑓: 0.00052 ( 3 hom. )

Consequence

CCDC141
NM_173648.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.54

Variant links:

Genes affected

CCDC141 (HGNC:26821): (coiled-coil domain containing 141) Predicted to be involved in axon guidance and cell adhesion. Predicted to act upstream of or within centrosome localization and cerebral cortex radially oriented cell migration. Predicted to be located in centrosome; cytoplasm; and plasma membrane. Predicted to be active in neuron projection. [provided by Alliance of Genome Resources, Apr 2022]

CCDC141 links:

(HGNC:):

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=0.0074644983).

BP6

Variant 2-178834304-C-T is Benign according to our data. Variant chr2-178834304-C-T is described in ClinVar as [Benign]. Clinvar id is 2714725.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC141	NM_173648.4 linkuse as main transcript	c.4462G>A	p.Gly1488Ser	missense_variant	24/24	ENST00000443758.7	NP_775919.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC141	ENST00000443758.7 linkuse as main transcript	c.4462G>A	p.Gly1488Ser	missense_variant	24/24	5	NM_173648.4	ENSP00000390190	P1	Q6ZP82-2
	ENST00000652826.1 linkuse as main transcript	n.306+5650C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00155

AC:

236

AN:

152064

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000966

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00599

Gnomad SAS

AF:

0.000623

Gnomad FIN

AF:

0.0173

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000191

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00145

AC:

199

AN:

137222

Hom.:

AF XY:

0.00154

AC XY:

115

AN XY:

74532

show subpopulations

Gnomad AFR exome

AF:

0.000154

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.000241

Gnomad EAS exome

AF:

0.00647

Gnomad SAS exome

AF:

0.000489

Gnomad FIN exome

AF:

0.0142

Gnomad NFE exome

AF:

0.000186

Gnomad OTH exome

AF:

0.00190

GnomAD4 exome

AF:

0.000517

AC:

715

AN:

1383770

Hom.:

Cov.:

AF XY:

0.000511

AC XY:

349

AN XY:

682834

show subpopulations

Gnomad4 AFR exome

AF:

0.0000633

Gnomad4 AMR exome

AF:

0.0000280

Gnomad4 ASJ exome

AF:

0.000437

Gnomad4 EAS exome

AF:

0.00291

Gnomad4 SAS exome

AF:

0.000530

Gnomad4 FIN exome

AF:

0.0119

Gnomad4 NFE exome

AF:

0.000101

Gnomad4 OTH exome

AF:

0.000725

GnomAD4 genome

AF:

0.00155

AC:

236

AN:

152182

Hom.:

Cov.:

AF XY:

0.00245

AC XY:

182

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0000963

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.00601

Gnomad4 SAS

AF:

0.000624

Gnomad4 FIN

AF:

0.0173

Gnomad4 NFE

AF:

0.000191

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000510

Hom.:

Bravo

AF:

0.000468

ExAC

AF:

0.00196

AC:

Asia WGS

AF:

0.00462

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 19, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.26

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Pathogenic

0.82

Eigen_PC

Pathogenic

0.76

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.63

MetaRNN

Benign

0.0075

MetaSVM

Uncertain

-0.18

MutationTaster

Benign

0.99

PrimateAI

Uncertain

0.48

ClinPred

0.10

GERP RS

5.8

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