rs193920889
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014320.3(HEBP2):āc.125A>Gā(p.His42Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,460,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_014320.3 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 |
---|---|---|---|---|---|---|---|
HEBP2 | NM_014320.3 | c.125A>G | p.His42Arg | missense_variant | 2/4 | ENST00000607197.6 | |
HEBP2 | NM_001326380.2 | c.158A>G | p.His53Arg | missense_variant | 2/4 | ||
HEBP2 | NM_001326381.2 | c.125A>G | p.His42Arg | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEBP2 | ENST00000607197.6 | c.125A>G | p.His42Arg | missense_variant | 2/4 | 1 | NM_014320.3 | P1 | |
HEBP2 | ENST00000448741.5 | c.158A>G | p.His53Arg | missense_variant | 2/4 | 5 | |||
HEBP2 | ENST00000367697.7 | c.125A>G | p.His42Arg | missense_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250478Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135414
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1460952Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726750
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at