rs6772967

Variant summary

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

The ENST00000328376.9(APRG1):​n.498+2984A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,954 control chromosomes in the GnomAD database, including 15,004 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 0.43 ( 15004 hom., cov: 31)

Consequence

APRG1
ENST00000328376.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.468

Publications

5 publications found
Variant links:
Genes affected
APRG1 (HGNC:24082): (APRG1 tumor suppressor candidate) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
APRG1NR_126512.1 linkn.183+2984A>G intron_variant Intron 1 of 6
APRG1NR_126513.1 linkn.183+2984A>G intron_variant Intron 1 of 3
APRG1NR_126514.1 linkn.183+2984A>G intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
APRG1ENST00000328376.9 linkn.498+2984A>G intron_variant Intron 1 of 5 1
APRG1ENST00000332506.7 linkn.498+2984A>G intron_variant Intron 1 of 6 1
APRG1ENST00000425932.5 linkn.103-8495A>G intron_variant Intron 1 of 3 1

Frequencies

GnomAD3 genomes
AF:
0.434
AC:
65928
AN:
151836
Hom.:
14982
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.506
Gnomad AMI
AF:
0.527
Gnomad AMR
AF:
0.407
Gnomad ASJ
AF:
0.364
Gnomad EAS
AF:
0.0742
Gnomad SAS
AF:
0.256
Gnomad FIN
AF:
0.371
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.450
Gnomad OTH
AF:
0.423
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.434
AC:
65987
AN:
151954
Hom.:
15004
Cov.:
31
AF XY:
0.425
AC XY:
31589
AN XY:
74254
show subpopulations
African (AFR)
AF:
0.505
AC:
20940
AN:
41430
American (AMR)
AF:
0.408
AC:
6224
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.364
AC:
1264
AN:
3470
East Asian (EAS)
AF:
0.0742
AC:
384
AN:
5176
South Asian (SAS)
AF:
0.256
AC:
1230
AN:
4806
European-Finnish (FIN)
AF:
0.371
AC:
3911
AN:
10552
Middle Eastern (MID)
AF:
0.405
AC:
119
AN:
294
European-Non Finnish (NFE)
AF:
0.450
AC:
30549
AN:
67940
Other (OTH)
AF:
0.419
AC:
885
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1861
3722
5583
7444
9305
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
590
1180
1770
2360
2950
<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:
0.438
Hom.:
7740
Bravo
AF:
0.442
Asia WGS
AF:
0.189
AC:
657
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.71
DANN
Benign
0.41
PhyloP100
-0.47
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs6772967; hg19: chr3-37444134; API