chr1-41510639-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_024503.5(HIVEP3):c.7033G>A(p.Ala2345Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000416 in 1,541,770 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_024503.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP3 | NM_024503.5 | c.7033G>A | p.Ala2345Thr | missense_variant | 9/9 | ENST00000372583.6 | |
HIVEP3 | NM_001127714.3 | c.7030G>A | p.Ala2344Thr | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP3 | ENST00000372583.6 | c.7033G>A | p.Ala2345Thr | missense_variant | 9/9 | 1 | NM_024503.5 | P5 | |
HIVEP3 | ENST00000372584.5 | c.7030G>A | p.Ala2344Thr | missense_variant | 8/8 | 1 | A2 | ||
HIVEP3 | ENST00000643665.1 | c.7030G>A | p.Ala2344Thr | missense_variant | 8/8 | A2 | |||
HIVEP3 | ENST00000460604.1 | n.1960G>A | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00219 AC: 334AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000513 AC: 75AN: 146080Hom.: 0 AF XY: 0.000435 AC XY: 34AN XY: 78160
GnomAD4 exome AF: 0.000222 AC: 308AN: 1389416Hom.: 2 Cov.: 30 AF XY: 0.000206 AC XY: 141AN XY: 684082
GnomAD4 genome ? AF: 0.00219 AC: 334AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.00213 AC XY: 159AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 02, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at