NM_152510.4:c.52-470G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152510.4(HORMAD2):c.52-470G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,950 control chromosomes in the GnomAD database, including 23,591 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.55 ( 23591 hom., cov: 31)
Consequence
HORMAD2
NM_152510.4 intron
NM_152510.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.820
Publications
60 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HORMAD2 | ENST00000336726.11 | c.52-470G>A | intron_variant | Intron 2 of 10 | 1 | NM_152510.4 | ENSP00000336984.6 | |||
HORMAD2 | ENST00000403975.1 | c.52-470G>A | intron_variant | Intron 2 of 10 | 2 | ENSP00000385055.1 | ||||
HORMAD2 | ENST00000450612.5 | n.52-470G>A | intron_variant | Intron 2 of 8 | 5 | ENSP00000393415.1 | ||||
HORMAD2 | ENST00000491605.1 | n.47-470G>A | intron_variant | Intron 1 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.546 AC: 82924AN: 151832Hom.: 23544 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
82924
AN:
151832
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.546 AC: 83037AN: 151950Hom.: 23591 Cov.: 31 AF XY: 0.552 AC XY: 40981AN XY: 74264 show subpopulations
GnomAD4 genome
AF:
AC:
83037
AN:
151950
Hom.:
Cov.:
31
AF XY:
AC XY:
40981
AN XY:
74264
show subpopulations
African (AFR)
AF:
AC:
28755
AN:
41452
American (AMR)
AF:
AC:
9117
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
1801
AN:
3468
East Asian (EAS)
AF:
AC:
1539
AN:
5168
South Asian (SAS)
AF:
AC:
2934
AN:
4818
European-Finnish (FIN)
AF:
AC:
5640
AN:
10532
Middle Eastern (MID)
AF:
AC:
178
AN:
294
European-Non Finnish (NFE)
AF:
AC:
31317
AN:
67920
Other (OTH)
AF:
AC:
1175
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1841
3683
5524
7366
9207
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
712
1424
2136
2848
3560
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1766
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.