Variant X-153950585-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005334.3(HCFC1):c.5704-42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,098,077 control chromosomes in the GnomAD database, including 35,729 homozygotes. There are 90,561 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 7973 hom., 12973 hem., cov: 24)

Exomes 𝑓: 0.24 ( 27756 hom. 77588 hem. )

Consequence

HCFC1
NM_005334.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.194

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]

HCFC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant X-153950585-G-A is Benign according to our data. Variant chrX-153950585-G-A is described in ClinVar as [Benign]. Clinvar id is 1292119.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCFC1	NM_005334.3 linkuse as main transcript	c.5704-42C>T		intron_variant		ENST00000310441.12

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
HCFC1	ENST00000310441.12 linkuse as main transcript	c.5704-42C>T	intron_variant	1	NM_005334.3	P2	P51610-1
HCFC1	ENST00000369984.4 linkuse as main transcript	c.5839-42C>T	intron_variant	5		A2
HCFC1	ENST00000444191.5 linkuse as main transcript	c.1430-42C>T	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.382

AC:

42596

AN:

111543

Hom.:

7963

Cov.:

AF XY:

0.383

AC XY:

12927

AN XY:

33767

show subpopulations

Gnomad AFR

AF:

0.687

Gnomad AMI

AF:

0.0689

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.760

Gnomad SAS

AF:

0.597

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.349

Gnomad NFE

AF:

0.180

Gnomad OTH

AF:

0.401

GnomAD3 exomes

AF:

0.377

AC:

47413

AN:

125673

Hom.:

8894

AF XY:

0.348

AC XY:

14875

AN XY:

42789

show subpopulations

Gnomad AFR exome

AF:

0.701

Gnomad AMR exome

AF:

0.620

Gnomad ASJ exome

AF:

0.284

Gnomad EAS exome

AF:

0.761

Gnomad SAS exome

AF:

0.593

Gnomad FIN exome

AF:

0.186

Gnomad NFE exome

AF:

0.177

Gnomad OTH exome

AF:

0.326

GnomAD4 exome

AF:

0.242

AC:

238746

AN:

986480

Hom.:

27756

Cov.:

AF XY:

0.266

AC XY:

77588

AN XY:

292138

show subpopulations

Gnomad4 AFR exome

AF:

0.701

Gnomad4 AMR exome

AF:

0.604

Gnomad4 ASJ exome

AF:

0.292

Gnomad4 EAS exome

AF:

0.750

Gnomad4 SAS exome

AF:

0.577

Gnomad4 FIN exome

AF:

0.179

Gnomad4 NFE exome

AF:

0.175

Gnomad4 OTH exome

AF:

0.309

GnomAD4 genome

AF:

0.382

AC:

42656

AN:

111597

Hom.:

7973

Cov.:

AF XY:

0.383

AC XY:

12973

AN XY:

33831

show subpopulations

Gnomad4 AFR

AF:

0.687

Gnomad4 AMR

AF:

0.498

Gnomad4 ASJ

AF:

0.255

Gnomad4 EAS

AF:

0.760

Gnomad4 SAS

AF:

0.594

Gnomad4 FIN

AF:

0.175

Gnomad4 NFE

AF:

0.180

Gnomad4 OTH

AF:

0.411

Alfa

AF:

0.261

Hom.:

3844

Bravo

AF:

0.423

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.28

DANN

Benign

0.20

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