Genetic Variant CCDC171:p.Ser65Asn (chr9-15578865-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The NM_173550.4(CCDC171):c.194G>A(p.Ser65Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00817 in 1,613,186 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0085 ( 79 hom. )

Consequence

CCDC171
NM_173550.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.76

Variant links:

Genes affected

CCDC171 (HGNC:29828): (coiled-coil domain containing 171)

CCDC171 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=0.0063900054).

BP6

Variant 9-15578865-G-A is Benign according to our data. Variant chr9-15578865-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2659091.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC171	NM_173550.4 link	c.194G>A	p.Ser65Asn	missense_variant	Exon 4 of 26	ENST00000380701.8	NP_775821.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC171	ENST00000380701.8 link	c.194G>A	p.Ser65Asn	missense_variant	Exon 4 of 26	1	NM_173550.4	ENSP00000370077.3		Q6TFL3-1

Frequencies

GnomAD3 genomes

AF:

0.00543

AC:

826

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00413

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00603

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00928

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00557

AC:

1393

AN:

250236

Hom.:

AF XY:

0.00557

AC XY:

753

AN XY:

135258

show subpopulations

Gnomad AFR exome

AF:

0.00228

Gnomad AMR exome

AF:

0.00289

Gnomad ASJ exome

AF:

0.0000996

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000328

Gnomad FIN exome

AF:

0.00917

Gnomad NFE exome

AF:

0.00899

Gnomad OTH exome

AF:

0.00625

GnomAD4 exome

AF:

0.00845

AC:

12349

AN:

1460888

Hom.:

Cov.:

AF XY:

0.00824

AC XY:

5989

AN XY:

726792

show subpopulations

Gnomad4 AFR exome

AF:

0.00132

Gnomad4 AMR exome

AF:

0.00294

Gnomad4 ASJ exome

AF:

0.000230

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000139

Gnomad4 FIN exome

AF:

0.00826

Gnomad4 NFE exome

AF:

0.0101

Gnomad4 OTH exome

AF:

0.00729

GnomAD4 genome

AF:

0.00542

AC:

826

AN:

152298

Hom.:

Cov.:

AF XY:

0.00522

AC XY:

389

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00603

Gnomad4 NFE

AF:

0.00928

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00808

Hom.:

Bravo

AF:

0.00543

TwinsUK

AF:

0.00863

AC:

ALSPAC

AF:

0.00934

AC:

ESP6500AA

AF:

0.00318

AC:

ESP6500EA

AF:

0.00756

AC:

ExAC

AF:

0.00570

AC:

692

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00727

EpiControl

AF:

0.00701

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Mar 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CCDC171: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.027

Eigen

Benign

-0.31

Eigen_PC

Benign

-0.12

FATHMM_MKL

Benign

0.75

LIST_S2

Benign

0.75

M_CAP

Benign

0.0068

MetaRNN

Benign

0.0064

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.5

PrimateAI

Uncertain

0.48

PROVEAN

Benign

-0.39

REVEL

Benign

0.031

Sift

Benign

0.41

Sift4G

Benign

0.66

Polyphen

0.0060

Vest4

0.49

MVP

0.061

ClinPred

0.0088

GERP RS

4.3

Varity_R

0.081

gMVP

0.068

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