chr22-30122020-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152510.4(HORMAD2):c.625C>G(p.Leu209Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,824 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 (★).
Frequency
Consequence
NM_152510.4 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 |
---|---|---|---|---|---|---|---|
HORMAD2 | NM_152510.4 | c.625C>G | p.Leu209Val | missense_variant | 10/11 | ENST00000336726.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HORMAD2 | ENST00000336726.11 | c.625C>G | p.Leu209Val | missense_variant | 10/11 | 1 | NM_152510.4 | P1 | |
HORMAD2 | ENST00000403975.1 | c.625C>G | p.Leu209Val | missense_variant | 10/11 | 2 | P1 | ||
HORMAD2 | ENST00000450612.5 | c.*312C>G | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247296Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134088
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460824Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726608
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 05, 2023 | The c.625C>G (p.L209V) alteration is located in exon 10 (coding exon 9) of the HORMAD2 gene. This alteration results from a C to G substitution at nucleotide position 625, causing the leucine (L) at amino acid position 209 to be replaced by a valine (V). 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