Variant 3-58884595-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001394063.1(CFAP20DC):c.665G>A(p.Arg222His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,613,784 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0073 ( 10 hom., cov: 32)

Exomes 𝑓: 0.011 ( 121 hom. )

Consequence

CFAP20DC
NM_001394063.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.678

Variant links:

Genes affected

CFAP20DC (HGNC:24763): (CFAP20 domain containing)

CFAP20DC links:

CFAP20DC-AS1 (HGNC:41063): (CFAP20DC antisense RNA 1)

CFAP20DC-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007875681).

BP6

Variant 3-58884595-C-T is Benign according to our data. Variant chr3-58884595-C-T is described in ClinVar as [Benign]. Clinvar id is 774300.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP20DC	NM_001394063.1 link	c.665G>A	p.Arg222His	missense_variant	7/17	ENST00000482387.7	NP_001380992.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP20DC	ENST00000482387.7 link	c.665G>A	p.Arg222His	missense_variant	7/17	5	NM_001394063.1	ENSP00000417122.2		A0A2U3TZK7

Frequencies

GnomAD3 genomes

AF:

0.00727

AC:

1105

AN:

152036

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00727

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0106

Gnomad FIN

AF:

0.00633

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0117

Gnomad OTH

AF:

0.00525

GnomAD3 exomes

AF:

0.00739

AC:

1859

AN:

251390

Hom.:

AF XY:

0.00809

AC XY:

1099

AN XY:

135862

show subpopulations

Gnomad AFR exome

AF:

0.00178

Gnomad AMR exome

AF:

0.00243

Gnomad ASJ exome

AF:

0.00149

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00964

Gnomad FIN exome

AF:

0.00795

Gnomad NFE exome

AF:

0.0108

Gnomad OTH exome

AF:

0.00619

GnomAD4 exome

AF:

0.0113

AC:

16508

AN:

1461630

Hom.:

121

Cov.:

AF XY:

0.0114

AC XY:

8260

AN XY:

727126

show subpopulations

Gnomad4 AFR exome

AF:

0.00149

Gnomad4 AMR exome

AF:

0.00244

Gnomad4 ASJ exome

AF:

0.00138

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0118

Gnomad4 FIN exome

AF:

0.00889

Gnomad4 NFE exome

AF:

0.0128

Gnomad4 OTH exome

AF:

0.00871

GnomAD4 genome

AF:

0.00726

AC:

1104

AN:

152154

Hom.:

Cov.:

AF XY:

0.00706

AC XY:

525

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00727

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0104

Gnomad4 FIN

AF:

0.00633

Gnomad4 NFE

AF:

0.0117

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00985

Hom.:

Bravo

AF:

0.00665

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.0108

AC:

ExAC

AF:

0.00739

AC:

897

Asia WGS

AF:

0.00549

AC:

AN:

3478

EpiCase

AF:

0.0104

EpiControl

AF:

0.00925

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Uncertain

1.0

Eigen

Benign

-0.54

Eigen_PC

Benign

-0.43

FATHMM_MKL

Benign

0.46

LIST_S2

Benign

0.84

T;T;T

MetaRNN

Benign

0.0079

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.1

L;.;.

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.65

N;.;N

REVEL

Benign

0.0050

Sift

Benign

0.26

T;.;T

Sift4G

Benign

0.36

T;.;T

Polyphen

0.045

B;.;B

Vest4

0.22

MVP

0.28

MPC

0.19

ClinPred

0.0059

GERP RS

1.8

gMVP

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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