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15-82540460-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The 15-82540460-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,586,436 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 2 hom. )

Consequence

RPS17
NM_001021.6 upstream_gene

Scores

1
1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.863
Variant links:
Genes affected
RPS17 (HGNC:10397): (ribosomal protein S17) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of four RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S17E family of ribosomal proteins and is located in the cytoplasm. Mutations in this gene cause Diamond-Blackfan anemia 4. Alternative splicing of this gene results in multiple transcript variants. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Apr 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
Variant 15-82540460-G-A is Benign according to our data. Variant chr15-82540460-G-A is described in ClinVar as [Benign]. Clinvar id is 1686317.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd at 122 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS17NM_001021.6 linkuse as main transcript upstream_gene_variant ENST00000647841.1
RPS17NR_111943.2 linkuse as main transcript upstream_gene_variant
RPS17NR_111944.3 linkuse as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS17ENST00000647841.1 linkuse as main transcript upstream_gene_variant NM_001021.6 P1

Frequencies

GnomAD3 genomes
AF:
0.000802
AC:
122
AN:
152144
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000620
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000985
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000793
AC:
69
AN:
86998
Hom.:
0
AF XY:
0.000946
AC XY:
44
AN XY:
46496
show subpopulations
Gnomad AFR exome
AF:
0.000172
Gnomad AMR exome
AF:
0.00180
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00116
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000861
Gnomad OTH exome
AF:
0.000789
GnomAD4 exome
AF:
0.00106
AC:
1520
AN:
1434174
Hom.:
2
Cov.:
32
AF XY:
0.00107
AC XY:
759
AN XY:
710206
show subpopulations
Gnomad4 AFR exome
AF:
0.000360
Gnomad4 AMR exome
AF:
0.00125
Gnomad4 ASJ exome
AF:
0.0000787
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00134
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00117
Gnomad4 OTH exome
AF:
0.00113
GnomAD4 genome
AF:
0.000795
AC:
121
AN:
152262
Hom.:
0
Cov.:
33
AF XY:
0.000846
AC XY:
63
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.000217
Gnomad4 AMR
AF:
0.00261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000985
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.000697
Hom.:
0
Bravo
AF:
0.000722

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingMendelicsMay 04, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.33
Cadd
Benign
15
Dann
Uncertain
0.98

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.13
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs575115395; hg19: chr15-83209211; API