19-7665708-G-A

Variant summary

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

The XR_007067117.1(RPS27AP19):​n.30G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 279,458 control chromosomes in the GnomAD database, including 937 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 0.089 ( 803 hom., cov: 32)
Exomes 𝑓: 0.039 ( 134 hom. )

Consequence

RPS27AP19
XR_007067117.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0120

Publications

1 publications found
Variant links:
Genes affected
RPS27AP19 (HGNC:52298): (RPS27A pseudogene 19)

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=-0.86).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RPS27AP19XR_007067117.1 linkn.30G>A non_coding_transcript_exon_variant Exon 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RPS27AP19ENST00000597285.1 linkn.-9G>A upstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.0892
AC:
13556
AN:
152006
Hom.:
800
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0217
Gnomad AMI
AF:
0.0702
Gnomad AMR
AF:
0.143
Gnomad ASJ
AF:
0.136
Gnomad EAS
AF:
0.0106
Gnomad SAS
AF:
0.113
Gnomad FIN
AF:
0.125
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.115
Gnomad OTH
AF:
0.0944
GnomAD4 exome
AF:
0.0391
AC:
4973
AN:
127334
Hom.:
134
Cov.:
0
AF XY:
0.0391
AC XY:
3000
AN XY:
76694
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00491
AC:
16
AN:
3260
American (AMR)
AF:
0.0602
AC:
454
AN:
7542
Ashkenazi Jewish (ASJ)
AF:
0.0429
AC:
168
AN:
3914
East Asian (EAS)
AF:
0.00528
AC:
26
AN:
4920
South Asian (SAS)
AF:
0.0459
AC:
1180
AN:
25720
European-Finnish (FIN)
AF:
0.0501
AC:
275
AN:
5494
Middle Eastern (MID)
AF:
0.0273
AC:
12
AN:
440
European-Non Finnish (NFE)
AF:
0.0376
AC:
2636
AN:
70062
Other (OTH)
AF:
0.0344
AC:
206
AN:
5982
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.383
Heterozygous variant carriers
0
254
507
761
1014
1268
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0891
AC:
13561
AN:
152124
Hom.:
803
Cov.:
32
AF XY:
0.0896
AC XY:
6660
AN XY:
74370
show subpopulations
African (AFR)
AF:
0.0217
AC:
900
AN:
41522
American (AMR)
AF:
0.144
AC:
2192
AN:
15252
Ashkenazi Jewish (ASJ)
AF:
0.136
AC:
471
AN:
3472
East Asian (EAS)
AF:
0.0102
AC:
53
AN:
5180
South Asian (SAS)
AF:
0.113
AC:
544
AN:
4816
European-Finnish (FIN)
AF:
0.125
AC:
1318
AN:
10584
Middle Eastern (MID)
AF:
0.0850
AC:
25
AN:
294
European-Non Finnish (NFE)
AF:
0.115
AC:
7798
AN:
67984
Other (OTH)
AF:
0.0930
AC:
196
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
640
1281
1921
2562
3202
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
158
316
474
632
790
<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:
0.0791
Hom.:
247
Bravo
AF:
0.0895
Asia WGS
AF:
0.0520
AC:
180
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
5.1
DANN
Benign
0.67
PhyloP100
-0.012

Splicing

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

Publications

Other links and lift over

dbSNP: rs12460483; hg19: chr19-7730594; API