rs2228210
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002114.4(HIVEP1):āc.2146A>Gā(p.Thr716Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 1,613,794 control chromosomes in the GnomAD database, including 90,091 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. 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 -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HIVEP1 | NM_002114.4 | c.2146A>G | p.Thr716Ala | missense_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.2146A>G | p.Thr716Ala | missense_variant | 4/9 | 1 | NM_002114.4 | ENSP00000368698 | P2 | |
HIVEP1 | ENST00000541134.5 | c.2146A>G | p.Thr716Ala | missense_variant | 4/9 | 5 | ENSP00000445617 | A2 | ||
HIVEP1 | ENST00000627968.2 | c.-4158A>G | 5_prime_UTR_variant | 4/8 | 5 | ENSP00000486543 | ||||
HIVEP1 | ENST00000442081.6 | c.166+2007A>G | intron_variant | 3 | ENSP00000409078 |
Frequencies
GnomAD3 genomes AF: 0.257 AC: 39066AN: 151946Hom.: 6171 Cov.: 32
GnomAD3 exomes AF: 0.301 AC: 74911AN: 248896Hom.: 12260 AF XY: 0.307 AC XY: 41541AN XY: 135094
GnomAD4 exome AF: 0.334 AC: 488143AN: 1461730Hom.: 83928 Cov.: 47 AF XY: 0.333 AC XY: 242491AN XY: 727160
GnomAD4 genome AF: 0.257 AC: 39045AN: 152064Hom.: 6163 Cov.: 32 AF XY: 0.254 AC XY: 18878AN XY: 74298
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at