3-58884595-C-T

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

1
15

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

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
CFAP20DCNM_001394063.1 linkc.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
CFAP20DCENST00000482387.7 linkc.665G>A p.Arg222His missense_variant 7/175 NM_001394063.1 ENSP00000417122.2 A0A2U3TZK7

Frequencies

GnomAD3 genomes
AF:
0.00727
AC:
1105
AN:
152036
Hom.:
10
Cov.:
32
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.:
12
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.:
31
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.:
10
Cov.:
32
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.:
8
Bravo
AF:
0.00665
ESP6500AA
AF:
0.00227
AC:
10
ESP6500EA
AF:
0.0108
AC:
93
ExAC
AF:
0.00739
AC:
897
Asia WGS
AF:
0.00549
AC:
19
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpApr 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.60
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
16
DANN
Uncertain
1.0
Eigen
Benign
-0.54
Eigen_PC
Benign
-0.43
FATHMM_MKL
Benign
0.46
N
LIST_S2
Benign
0.84
T;T;T
MetaRNN
Benign
0.0079
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.1
L;.;.
PrimateAI
Benign
0.29
T
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
T
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.

Other links and lift over

dbSNP: rs116534917; hg19: chr3-58870321; API