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15-82540294-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001021.6(RPS17):c.3+132C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 1,586,162 control chromosomes in the GnomAD database, including 2,556 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.074 ( 639 hom., cov: 33)
Exomes 𝑓: 0.044 ( 1917 hom. )

Consequence

RPS17
NM_001021.6 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.168
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 15-82540294-G-C is Benign according to our data. Variant chr15-82540294-G-C is described in ClinVar as [Benign]. Clinvar id is 1235999.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS17NM_001021.6 linkuse as main transcriptc.3+132C>G intron_variant ENST00000647841.1
RPS17NR_111943.2 linkuse as main transcriptn.164C>G non_coding_transcript_exon_variant 1/4
RPS17NR_111944.3 linkuse as main transcriptn.32+132C>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS17ENST00000647841.1 linkuse as main transcriptc.3+132C>G intron_variant NM_001021.6 P1

Frequencies

GnomAD3 genomes
AF:
0.0743
AC:
11313
AN:
152174
Hom.:
637
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.150
Gnomad AMI
AF:
0.0910
Gnomad AMR
AF:
0.0718
Gnomad ASJ
AF:
0.0484
Gnomad EAS
AF:
0.00232
Gnomad SAS
AF:
0.0503
Gnomad FIN
AF:
0.0551
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0402
Gnomad OTH
AF:
0.0674
GnomAD4 exome
AF:
0.0443
AC:
63458
AN:
1433870
Hom.:
1917
Cov.:
31
AF XY:
0.0435
AC XY:
30947
AN XY:
711546
show subpopulations
Gnomad4 AFR exome
AF:
0.162
Gnomad4 AMR exome
AF:
0.0973
Gnomad4 ASJ exome
AF:
0.0448
Gnomad4 EAS exome
AF:
0.00100
Gnomad4 SAS exome
AF:
0.0440
Gnomad4 FIN exome
AF:
0.0550
Gnomad4 NFE exome
AF:
0.0396
Gnomad4 OTH exome
AF:
0.0487
GnomAD4 genome
AF:
0.0744
AC:
11330
AN:
152292
Hom.:
639
Cov.:
33
AF XY:
0.0737
AC XY:
5488
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.151
Gnomad4 AMR
AF:
0.0717
Gnomad4 ASJ
AF:
0.0484
Gnomad4 EAS
AF:
0.00232
Gnomad4 SAS
AF:
0.0497
Gnomad4 FIN
AF:
0.0551
Gnomad4 NFE
AF:
0.0402
Gnomad4 OTH
AF:
0.0667
Alfa
AF:
0.00750
Hom.:
10
Bravo
AF:
0.0807

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxSep 15, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
3.0
Dann
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs542153649; hg19: chr15-83209045; API