6-12120852-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002114.4(HIVEP1):c.1057G>T(p.Asp353Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP1 | NM_002114.4 | c.1057G>T | p.Asp353Tyr | missense_variant | 4/9 | ENST00000379388.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP1 | ENST00000379388.7 | c.1057G>T | p.Asp353Tyr | missense_variant | 4/9 | 1 | NM_002114.4 | P2 | |
HIVEP1 | ENST00000541134.5 | c.1057G>T | p.Asp353Tyr | missense_variant | 4/9 | 5 | A2 | ||
HIVEP1 | ENST00000627968.2 | c.-5247G>T | 5_prime_UTR_variant | 4/8 | 5 | ||||
HIVEP1 | ENST00000442081.6 | c.166+918G>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000762 AC: 19AN: 249498Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135356
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461858Hom.: 0 Cov.: 37 AF XY: 0.0000564 AC XY: 41AN XY: 727228
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 08, 2023 | The c.1057G>T (p.D353Y) alteration is located in exon 4 (coding exon 3) of the HIVEP1 gene. This alteration results from a G to T substitution at nucleotide position 1057, causing the aspartic acid (D) at amino acid position 353 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at