6-12120573-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_002114.4(HIVEP1):c.778A>C(p.Thr260Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002114.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP1 | NM_002114.4 | c.778A>C | p.Thr260Pro | missense_variant | 4/9 | ENST00000379388.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP1 | ENST00000379388.7 | c.778A>C | p.Thr260Pro | missense_variant | 4/9 | 1 | NM_002114.4 | P2 | |
HIVEP1 | ENST00000541134.5 | c.778A>C | p.Thr260Pro | missense_variant | 4/9 | 5 | A2 | ||
HIVEP1 | ENST00000627968.2 | c.-5526A>C | 5_prime_UTR_variant | 4/8 | 5 | ||||
HIVEP1 | ENST00000442081.6 | c.166+639A>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461870Hom.: 0 Cov.: 37 AF XY: 0.0000165 AC XY: 12AN XY: 727236
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
HIVEP1-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 03, 2023 | The HIVEP1 c.778A>C variant is predicted to result in the amino acid substitution p.Thr260Pro. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at