chr6-12120732-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002114.4(HIVEP1):āc.937A>Cā(p.Asn313His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002114.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIVEP1 | NM_002114.4 | c.937A>C | p.Asn313His | missense_variant | 4/9 | ENST00000379388.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP1 | ENST00000379388.7 | c.937A>C | p.Asn313His | missense_variant | 4/9 | 1 | NM_002114.4 | P2 | |
HIVEP1 | ENST00000541134.5 | c.937A>C | p.Asn313His | missense_variant | 4/9 | 5 | A2 | ||
HIVEP1 | ENST00000627968.2 | c.-5367A>C | 5_prime_UTR_variant | 4/8 | 5 | ||||
HIVEP1 | ENST00000442081.6 | c.166+798A>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461880Hom.: 0 Cov.: 37 AF XY: 0.00000275 AC XY: 2AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2022 | The c.937A>C (p.N313H) alteration is located in exon 4 (coding exon 3) of the HIVEP1 gene. This alteration results from a A to C substitution at nucleotide position 937, causing the asparagine (N) at amino acid position 313 to be replaced by a histidine (H). 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