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GeneBe

rs1061170

chr1-196690107-C-Achr1-196690107-C-Gchr1-196690107-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate

The NM_000186.4(CFH):c.1204C>A(p.His402Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H402Y) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)

Consequence

CFH
NM_000186.4 missense

Scores

17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -8.33

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 31.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.12425029).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CFHNM_000186.4 linkuse as main transcriptc.1204C>A p.His402Asn missense_variant 9/22 ENST00000367429.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CFHENST00000367429.9 linkuse as main transcriptc.1204C>A p.His402Asn missense_variant 9/221 NM_000186.4 P2

Frequencies

GnomAD3 genomes
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.71
Cadd
Benign
0.0010
Dann
Benign
0.34
Eigen
Benign
-2.7
Eigen_PC
Benign
-2.8
FATHMM_MKL
Benign
0.0031
N
LIST_S2
Benign
0.12
T;T;T
M_CAP
Benign
0.050
D
MetaRNN
Benign
0.12
T;T;T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-0.10
N;.;N
REVEL
Benign
0.067
Sift
Benign
0.53
T;.;T
Sift4G
Benign
0.32
T;T;T
Polyphen
0.0
.;.;B
Vest4
0.12
MutPred
0.57
Loss of catalytic residue at H402 (P = 0.0361);Loss of catalytic residue at H402 (P = 0.0361);.;
MVP
0.43
MPC
0.15
ClinPred
0.018
T
GERP RS
-9.1
gMVP
0.57

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: rs1061170; hg19: chr1-196659237;