chr15-82536888-C-T

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001021.6(RPS17):​c.328-7G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00232 in 1,613,936 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0020 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 4 hom. )

Consequence

RPS17
NM_001021.6 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.00005533
2

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.739
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 15-82536888-C-T is Benign according to our data. Variant chr15-82536888-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 506484.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 312 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS17NM_001021.6 linkuse as main transcriptc.328-7G>A splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000647841.1
RPS17NR_111943.2 linkuse as main transcriptn.650-7G>A splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant
RPS17NR_111944.3 linkuse as main transcriptn.478-7G>A splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS17ENST00000647841.1 linkuse as main transcriptc.328-7G>A splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant NM_001021.6 P1

Frequencies

GnomAD3 genomes
AF:
0.00205
AC:
312
AN:
152162
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000290
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000327
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00538
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00328
Gnomad OTH
AF:
0.00144
GnomAD4 exome
AF:
0.00235
AC:
3428
AN:
1461656
Hom.:
4
Cov.:
31
AF XY:
0.00237
AC XY:
1720
AN XY:
727138
show subpopulations
Gnomad4 AFR exome
AF:
0.000269
Gnomad4 AMR exome
AF:
0.000201
Gnomad4 ASJ exome
AF:
0.00348
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.000452
Gnomad4 FIN exome
AF:
0.00603
Gnomad4 NFE exome
AF:
0.00256
Gnomad4 OTH exome
AF:
0.00182
GnomAD4 genome
AF:
0.00205
AC:
312
AN:
152280
Hom.:
2
Cov.:
32
AF XY:
0.00212
AC XY:
158
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.000289
Gnomad4 AMR
AF:
0.000327
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00538
Gnomad4 NFE
AF:
0.00328
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00199
Hom.:
1
Bravo
AF:
0.00143

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 16, 2021- -
Diamond-Blackfan anemia 4 Benign:1
Likely benign, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsAug 04, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.0
DANN
Benign
0.87

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000055
dbscSNV1_RF
Benign
0.0060
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: rs975130647; hg19: chr15-83205639; API