chr6-12120880-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002114.4(HIVEP1):c.1085C>T(p.Pro362Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,614,122 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002114.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP1 | NM_002114.4 | c.1085C>T | p.Pro362Leu | missense_variant | 4/9 | ENST00000379388.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP1 | ENST00000379388.7 | c.1085C>T | p.Pro362Leu | missense_variant | 4/9 | 1 | NM_002114.4 | P2 | |
HIVEP1 | ENST00000541134.5 | c.1085C>T | p.Pro362Leu | missense_variant | 4/9 | 5 | A2 | ||
HIVEP1 | ENST00000627968.2 | c.-5219C>T | 5_prime_UTR_variant | 4/8 | 5 | ||||
HIVEP1 | ENST00000442081.6 | c.166+946C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0118 AC: 1801AN: 152136Hom.: 33 Cov.: 32
GnomAD3 exomes AF: 0.00309 AC: 771AN: 249514Hom.: 14 AF XY: 0.00214 AC XY: 290AN XY: 135360
GnomAD4 exome AF: 0.00130 AC: 1903AN: 1461868Hom.: 41 Cov.: 37 AF XY: 0.00113 AC XY: 825AN XY: 727234
GnomAD4 genome ? AF: 0.0119 AC: 1805AN: 152254Hom.: 33 Cov.: 32 AF XY: 0.0114 AC XY: 850AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at