X-153949406-A-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005334.3(HCFC1):c.6069-20T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000325 in 1,198,834 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.000035 ( 0 hom. 13 hem. )
Consequence
HCFC1
NM_005334.3 intron
NM_005334.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.146
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant X-153949406-A-G is Benign according to our data. Variant chrX-153949406-A-G is described in ClinVar as [Benign]. Clinvar id is 2716475.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAdExome4 at 13 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.6069-20T>C | intron_variant | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.6069-20T>C | intron_variant | 1 | NM_005334.3 | P2 | |||
HCFC1 | ENST00000369984.4 | c.6204-20T>C | intron_variant | 5 | A2 | ||||
HCFC1 | ENST00000444191.5 | c.1795-20T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000902 AC: 1AN: 110908Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33116
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GnomAD3 exomes AF: 0.0000614 AC: 11AN: 179138Hom.: 0 AF XY: 0.0000458 AC XY: 3AN XY: 65500
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GnomAD4 exome AF: 0.0000349 AC: 38AN: 1087926Hom.: 0 Cov.: 29 AF XY: 0.0000367 AC XY: 13AN XY: 353920
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GnomAD4 genome AF: 0.00000902 AC: 1AN: 110908Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33116
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at