ENST00000596329.3:n.515-1643C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000596329.3(HRG-AS1):​n.515-1643C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,992 control chromosomes in the GnomAD database, including 2,550 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 0.18 ( 2550 hom., cov: 31)

Consequence

HRG-AS1
ENST00000596329.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252

Publications

16 publications found
Variant links:
Genes affected
HRG-AS1 (HGNC:55915): (HRG and FETUB antisense RNA 1)

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=-0.68).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HRG-AS1ENST00000596329.3 linkn.515-1643C>T intron_variant Intron 1 of 2 5
HRG-AS1ENST00000596632.1 linkn.432-3261C>T intron_variant Intron 1 of 2 5
HRG-AS1ENST00000599314.5 linkn.61-4622C>T intron_variant Intron 1 of 5 5

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27287
AN:
151874
Hom.:
2552
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.201
Gnomad AMI
AF:
0.148
Gnomad AMR
AF:
0.138
Gnomad ASJ
AF:
0.131
Gnomad EAS
AF:
0.281
Gnomad SAS
AF:
0.148
Gnomad FIN
AF:
0.192
Gnomad MID
AF:
0.0791
Gnomad NFE
AF:
0.173
Gnomad OTH
AF:
0.152
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.180
AC:
27300
AN:
151992
Hom.:
2550
Cov.:
31
AF XY:
0.181
AC XY:
13461
AN XY:
74298
show subpopulations
African (AFR)
AF:
0.200
AC:
8311
AN:
41470
American (AMR)
AF:
0.138
AC:
2094
AN:
15220
Ashkenazi Jewish (ASJ)
AF:
0.131
AC:
455
AN:
3462
East Asian (EAS)
AF:
0.281
AC:
1451
AN:
5164
South Asian (SAS)
AF:
0.149
AC:
719
AN:
4822
European-Finnish (FIN)
AF:
0.192
AC:
2025
AN:
10562
Middle Eastern (MID)
AF:
0.0782
AC:
23
AN:
294
European-Non Finnish (NFE)
AF:
0.173
AC:
11769
AN:
67978
Other (OTH)
AF:
0.151
AC:
319
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1097
2194
3290
4387
5484
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
290
580
870
1160
1450
<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:
0.174
Hom.:
9963
Bravo
AF:
0.176
Asia WGS
AF:
0.192
AC:
666
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
13
DANN
Benign
0.83
PhyloP100
0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1656966; hg19: chr3-186466252; API