rs12211360
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006734.4(HIVEP2):c.-527-15080T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,186 control chromosomes in the GnomAD database, including 1,376 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.12 ( 1376 hom., cov: 32)
Consequence
HIVEP2
NM_006734.4 intron
NM_006734.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.67
Genes affected
HIVEP2 (HGNC:4921): (HIVEP zinc finger 2) This gene encodes a member of a family of closely related, large, zinc finger-containing transcription factors. The encoded protein regulates transcription by binding to regulatory regions of various cellular and viral genes that maybe involved in growth, development and metastasis. The protein contains the ZAS domain comprised of two widely separated regions of zinc finger motifs, a stretch of highly acidic amino acids and a serine/threonine-rich sequence. [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP2 | NM_006734.4 | c.-527-15080T>C | intron_variant | ENST00000367603.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP2 | ENST00000367603.8 | c.-527-15080T>C | intron_variant | 1 | NM_006734.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.119 AC: 18120AN: 152066Hom.: 1378 Cov.: 32
GnomAD3 genomes
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18120
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152066
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.119 AC: 18101AN: 152186Hom.: 1376 Cov.: 32 AF XY: 0.118 AC XY: 8759AN XY: 74394
GnomAD4 genome
?
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18101
AN:
152186
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32
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8759
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74394
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Asia WGS
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337
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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