6-12120710-A-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_002114.4(HIVEP1):āc.915A>Gā(p.Ser305Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,614,250 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: š 0.00058 ( 0 hom., cov: 32)
Exomes š: 0.000059 ( 0 hom. )
Consequence
HIVEP1
NM_002114.4 synonymous
NM_002114.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.485
Genes affected
HIVEP1 (HGNC:4920): (HIVEP zinc finger 1) This gene encodes a transcription factor belonging to the ZAS family, members of which are large proteins that contain a ZAS domain - a modular protein structure consisting of a pair of C2H2 zinc fingers with an acidic-rich region and a serine/threonine-rich sequence. These proteins bind specifically to the DNA sequence motif, GGGACTTTCC, found in the enhancer elements of several viral promoters, including human immunodeficiency virus (HIV), and to related sequences found in the enhancer elements of a number of cellular promoters. This protein binds to this sequence motif, suggesting a role in the transcriptional regulation of both viral and cellular genes. [provided by RefSeq, Oct 2011]
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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=-0.89).
BP6
Variant 6-12120710-A-G is Benign according to our data. Variant chr6-12120710-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3052158.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.485 with no splicing effect.
BS2
High AC in GnomAd4 at 88 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HIVEP1 | NM_002114.4 | c.915A>G | p.Ser305Ser | synonymous_variant | 4/9 | ENST00000379388.7 | NP_002105.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HIVEP1 | ENST00000379388.7 | c.915A>G | p.Ser305Ser | synonymous_variant | 4/9 | 1 | NM_002114.4 | ENSP00000368698.2 | ||
HIVEP1 | ENST00000541134.5 | c.915A>G | p.Ser305Ser | synonymous_variant | 4/9 | 5 | ||||
HIVEP1 | ENST00000627968 | c.-5389A>G | 5_prime_UTR_variant | 4/8 | 5 | ENSP00000486543.2 | ||||
HIVEP1 | ENST00000442081.6 | c.166+776A>G | intron_variant | 3 | ENSP00000409078.3 |
Frequencies
GnomAD3 genomes AF: 0.000578 AC: 88AN: 152254Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000164 AC: 41AN: 249524Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135366
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GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461878Hom.: 0 Cov.: 37 AF XY: 0.0000468 AC XY: 34AN XY: 727236
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GnomAD4 genome AF: 0.000578 AC: 88AN: 152372Hom.: 0 Cov.: 32 AF XY: 0.000550 AC XY: 41AN XY: 74506
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
HIVEP1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 29, 2022 | 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). - |
Computational scores
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BayesDel_noAF
Benign
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at