22-30098858-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_152510.4(HORMAD2):āc.58G>Cā(p.Val20Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0028 in 1,608,456 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_152510.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HORMAD2 | NM_152510.4 | c.58G>C | p.Val20Leu | missense_variant | 3/11 | ENST00000336726.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HORMAD2 | ENST00000336726.11 | c.58G>C | p.Val20Leu | missense_variant | 3/11 | 1 | NM_152510.4 | P1 | |
HORMAD2 | ENST00000403975.1 | c.58G>C | p.Val20Leu | missense_variant | 3/11 | 2 | P1 | ||
HORMAD2 | ENST00000491605.1 | n.53G>C | non_coding_transcript_exon_variant | 2/4 | 3 | ||||
HORMAD2 | ENST00000450612.5 | c.58G>C | p.Val20Leu | missense_variant, NMD_transcript_variant | 3/9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0148 AC: 2255AN: 152128Hom.: 59 Cov.: 32
GnomAD3 exomes AF: 0.00370 AC: 905AN: 244694Hom.: 22 AF XY: 0.00292 AC XY: 388AN XY: 132746
GnomAD4 exome AF: 0.00154 AC: 2241AN: 1456210Hom.: 48 Cov.: 30 AF XY: 0.00137 AC XY: 993AN XY: 724330
GnomAD4 genome AF: 0.0148 AC: 2260AN: 152246Hom.: 59 Cov.: 32 AF XY: 0.0145 AC XY: 1078AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 28, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at