rs376049260

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2

The NM_005334.3(HCFC1):​c.3492C>T​(p.Ser1164Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,169,225 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 414 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00079 ( 0 hom., 29 hem., cov: 24)
Exomes 𝑓: 0.0011 ( 0 hom. 385 hem. )

Consequence

HCFC1
NM_005334.3 synonymous

Scores

2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:6

Conservation

PhyloP100: -0.0830
Variant links:
Genes affected
HCFC1 (HGNC:4839): (host cell factor C1) This gene is a member of the host cell factor family and encodes a protein with five Kelch repeats, a fibronectin-like motif, and six HCF repeats, each of which contains a highly specific cleavage signal. This nuclear coactivator is proteolytically cleaved at one of the six possible sites, resulting in the creation of an N-terminal chain and the corresponding C-terminal chain. The final form of this protein consists of noncovalently bound N- and C-terminal chains. The protein is involved in control of the cell cycle and transcriptional regulation during herpes simplex virus infection. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

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 (BayesDel_noAF=-0.81).
BP6
Variant X-153954907-G-A is Benign according to our data. Variant chrX-153954907-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 211134.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Benign=1, Uncertain_significance=1}. Variant chrX-153954907-G-A is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-0.083 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 29 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HCFC1NM_005334.3 linkc.3492C>T p.Ser1164Ser synonymous_variant Exon 17 of 26 ENST00000310441.12 NP_005325.2 P51610-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HCFC1ENST00000310441.12 linkc.3492C>T p.Ser1164Ser synonymous_variant Exon 17 of 26 1 NM_005334.3 ENSP00000309555.7 P51610-1
HCFC1ENST00000369984.4 linkc.3492C>T p.Ser1164Ser synonymous_variant Exon 17 of 26 5 ENSP00000359001.4 A6NEM2

Frequencies

GnomAD3 genomes
AF:
0.000792
AC:
89
AN:
112331
Hom.:
0
Cov.:
24
AF XY:
0.000840
AC XY:
29
AN XY:
34519
show subpopulations
Gnomad AFR
AF:
0.000258
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000185
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000644
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00141
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000666
AC:
80
AN:
120161
Hom.:
0
AF XY:
0.000710
AC XY:
23
AN XY:
32401
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000480
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000736
Gnomad FIN exome
AF:
0.000417
Gnomad NFE exome
AF:
0.00144
Gnomad OTH exome
AF:
0.000305
GnomAD4 exome
AF:
0.00109
AC:
1152
AN:
1056841
Hom.:
0
Cov.:
34
AF XY:
0.00113
AC XY:
385
AN XY:
340155
show subpopulations
Gnomad4 AFR exome
AF:
0.000157
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000594
Gnomad4 FIN exome
AF:
0.000837
Gnomad4 NFE exome
AF:
0.00129
Gnomad4 OTH exome
AF:
0.00117
GnomAD4 genome
AF:
0.000792
AC:
89
AN:
112384
Hom.:
0
Cov.:
24
AF XY:
0.000839
AC XY:
29
AN XY:
34582
show subpopulations
Gnomad4 AFR
AF:
0.000258
Gnomad4 AMR
AF:
0.000184
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000644
Gnomad4 NFE
AF:
0.00142
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000651
Hom.:
4
Bravo
AF:
0.000722

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:6
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not specified Uncertain:1Benign:3
Sep 27, 2014
Genetic Services Laboratory, University of Chicago
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Nov 01, 2016
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 14, 2017
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

HCFC1-related disorder Benign:1
Feb 28, 2019
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Oct 08, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Benign:1
-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
4.3
DANN
Benign
0.62
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.8

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.

Other links and lift over

dbSNP: rs376049260; hg19: chrX-153220358; API