chr15-69304869-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017705.4(PAQR5):c.-277+5813A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0398 in 152,298 control chromosomes in the GnomAD database, including 177 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 0.040 ( 177 hom., cov: 32)
Consequence
PAQR5
NM_017705.4 intron
NM_017705.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.59
Publications
1 publications found
Genes affected
PAQR5 (HGNC:29645): (progestin and adipoQ receptor family member 5) Predicted to enable signaling receptor activity. Predicted to be involved in oogenesis. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAQR5 | NM_017705.4 | c.-277+5813A>G | intron_variant | Intron 1 of 8 | ENST00000395407.7 | NP_060175.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0398 AC: 6063AN: 152180Hom.: 176 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
6063
AN:
152180
Hom.:
Cov.:
32
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: 0.0398 AC: 6069AN: 152298Hom.: 177 Cov.: 32 AF XY: 0.0413 AC XY: 3077AN XY: 74456 show subpopulations
GnomAD4 genome
AF:
AC:
6069
AN:
152298
Hom.:
Cov.:
32
AF XY:
AC XY:
3077
AN XY:
74456
show subpopulations
African (AFR)
AF:
AC:
2117
AN:
41570
American (AMR)
AF:
AC:
913
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
104
AN:
3470
East Asian (EAS)
AF:
AC:
659
AN:
5180
South Asian (SAS)
AF:
AC:
181
AN:
4828
European-Finnish (FIN)
AF:
AC:
574
AN:
10608
Middle Eastern (MID)
AF:
AC:
14
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1403
AN:
68032
Other (OTH)
AF:
AC:
92
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
289
577
866
1154
1443
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
68
136
204
272
340
<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:
342
AN:
3478
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
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