Genetic Variant CFHR3:p.Arg39Cys (chr1-196779218-C-T) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_021023.6(CFHR3):c.115C>T(p.Arg39Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,529,148 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R39H) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00032 ( 4 hom., cov: 25)

Exomes 𝑓: 0.00010 ( 23 hom. )

Consequence

CFHR3
NM_021023.6 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.66

Variant links:

Genes affected

CFHR3 (HGNC:16980): (complement factor H related 3) The protein encoded by this gene is a secreted protein, which belongs to the complement factor H-related protein family. It binds to heparin, and may be involved in complement regulation. Mutations in this gene are associated with decreased risk of age-related macular degeneration, and with an increased risk of atypical hemolytic-uremic syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

CFHR3 links:

ENSG00000289697 (HGNC:):

ENSG00000289697 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0854373).

BS2

High Homozygotes in GnomAd4 at 4 AD,AR,Digenic gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFHR3	NM_021023.6 link	c.115C>T	p.Arg39Cys	missense_variant	Exon 2 of 6	ENST00000367425.9	NP_066303.2	Q02985-1
CFHR3	NM_001166624.2 link	c.115C>T	p.Arg39Cys	missense_variant	Exon 2 of 5		NP_001160096.1	Q02985-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFHR3	ENST00000367425.9 link	c.115C>T	p.Arg39Cys	missense_variant	Exon 2 of 6	1	NM_021023.6	ENSP00000356395.5		Q02985-1
ENSG00000289697	ENST00000696032.1 link	c.3637C>T	p.Arg1213Cys	missense_variant	Exon 23 of 27			ENSP00000512341.1		A0A8Q3SIA1

Frequencies

GnomAD3 genomes

AF:

0.000322

AC:

AN:

136844

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000306

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00225

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000155

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000147

AC:

AN:

238312

Hom.:

AF XY:

0.0000934

AC XY:

AN XY:

128468

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000498

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000735

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000147

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000101

AC:

141

AN:

1392190

Hom.:

Cov.:

AF XY:

0.000111

AC XY:

AN XY:

691454

show subpopulations

Gnomad4 AFR exome

AF:

0.000108

Gnomad4 AMR exome

AF:

0.000364

Gnomad4 ASJ exome

AF:

0.0000410

Gnomad4 EAS exome

AF:

0.000127

Gnomad4 SAS exome

AF:

0.0000652

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000104

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.000321

AC:

AN:

136958

Hom.:

Cov.:

AF XY:

0.000450

AC XY:

AN XY:

66602

show subpopulations

Gnomad4 AFR

AF:

0.0000305

Gnomad4 AMR

AF:

0.00225

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000196

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000155

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000113

Hom.:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000364

AC:

ExAC

AF:

0.0000433

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Nov 23, 2022

Mayo Clinic Laboratories, Mayo Clinic

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.52

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.37

CADD

Benign

6.7

DANN

Benign

0.79

DEOGEN2

Benign

0.15

T;T;.;T

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.00032

LIST_S2

Uncertain

0.91

D;.;D;D

M_CAP

Benign

0.047

MetaRNN

Benign

0.085

T;T;T;T

MetaSVM

Benign

-0.80

MutationAssessor

Benign

1.6

L;.;L;.

PrimateAI

Benign

0.40

PROVEAN

Uncertain

-2.6

D;D;D;.

REVEL

Benign

0.17

Sift

Uncertain

0.023

D;T;D;.

Sift4G

Benign

0.15

T;T;T;D

Polyphen

0.063

B;B;.;.

Vest4

0.18

MVP

0.54

MPC

0.12

ClinPred

0.053

GERP RS

-1.8

Varity_R

0.069

gMVP

0.70

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