GeneBe

rs10917688

Variant names:

Variant summary

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

The ENST00000729097.1(RPL31P11):​n.48-3780G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,140 control chromosomes in the GnomAD database, including 2,361 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 0.16 ( 2361 hom., cov: 31)

Consequence

RPL31P11
ENST00000729097.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.182

Publications

5 publications found
Variant links:
Genes affected

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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 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
RPL31P11ENST00000729097.1 linkn.48-3780G>A intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.156
AC:
23648
AN:
152022
Hom.:
2361
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0458
Gnomad AMI
AF:
0.0965
Gnomad AMR
AF:
0.177
Gnomad ASJ
AF:
0.186
Gnomad EAS
AF:
0.00770
Gnomad SAS
AF:
0.213
Gnomad FIN
AF:
0.176
Gnomad MID
AF:
0.263
Gnomad NFE
AF:
0.220
Gnomad OTH
AF:
0.167
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.156
AC:
23658
AN:
152140
Hom.:
2361
Cov.:
31
AF XY:
0.155
AC XY:
11526
AN XY:
74364
show subpopulations
African (AFR)
AF:
0.0458
AC:
1904
AN:
41546
American (AMR)
AF:
0.177
AC:
2702
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.186
AC:
644
AN:
3470
East Asian (EAS)
AF:
0.00772
AC:
40
AN:
5184
South Asian (SAS)
AF:
0.213
AC:
1023
AN:
4808
European-Finnish (FIN)
AF:
0.176
AC:
1860
AN:
10552
Middle Eastern (MID)
AF:
0.272
AC:
80
AN:
294
European-Non Finnish (NFE)
AF:
0.220
AC:
14959
AN:
67970
Other (OTH)
AF:
0.169
AC:
358
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
977
1954
2932
3909
4886
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
270
540
810
1080
1350
<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:
0.183
Hom.:
521
Bravo
AF:
0.147
Asia WGS
AF:
0.120
AC:
416
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.9
DANN
Benign
0.69
PhyloP100
0.18

Splicing

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

Publications

Other links and lift over

dbSNP: rs10917688; hg19: chr1-161658780; API