GeneBe

10-95595157-C-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000398190.2(RPS3AP36):​n.560C>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0000181 in 607,320 control chromosomes in the GnomAD database, including 1 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: not found (cov: 33)
Exomes 𝑓: 0.000018 ( 1 hom. )

Consequence

RPS3AP36
ENST00000398190.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.65

Publications

10 publications found
Variant links:
Genes affected
RPS3AP36 (HGNC:35596): (RPS3A pseudogene 36)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RPS3AP36 n.95595157C>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RPS3AP36ENST00000398190.2 linkn.560C>A non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.0000181
AC:
11
AN:
607320
Hom.:
1
Cov.:
4
AF XY:
0.0000301
AC XY:
10
AN XY:
331808
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
17254
American (AMR)
AF:
0.00
AC:
0
AN:
42282
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20572
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35904
South Asian (SAS)
AF:
0.000146
AC:
10
AN:
68562
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
37166
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4078
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
349032
Other (OTH)
AF:
0.0000308
AC:
1
AN:
32470
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
5.7
DANN
Benign
0.79
PhyloP100
3.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs498055; hg19: chr10-97354914; API