15-82540071-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001021.6(RPS17):​c.65C>T​(p.Thr22Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

RPS17
NM_001021.6 missense

Scores

7
5
7

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.84
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 Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.81

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RPS17NM_001021.6 linkc.65C>T p.Thr22Met missense_variant Exon 2 of 5 ENST00000647841.1 NP_001012.1 P08708
RPS17NR_111943.2 linkn.387C>T non_coding_transcript_exon_variant Exon 1 of 4
RPS17NR_111944.3 linkn.94C>T non_coding_transcript_exon_variant Exon 2 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RPS17ENST00000647841.1 linkc.65C>T p.Thr22Met missense_variant Exon 2 of 5 NM_001021.6 ENSP00000498019.1 P08708
ENSG00000260836ENST00000562833.2 linkc.1412C>T p.Thr471Met missense_variant Exon 10 of 13 3 ENSP00000454786.2 H3BNC9

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

Diamond-Blackfan anemia 4 Uncertain:1
Apr 03, 2024
Fulgent Genetics, Fulgent Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.87
BayesDel_addAF
Pathogenic
0.20
D
BayesDel_noAF
Uncertain
0.050
CADD
Uncertain
25
DANN
Benign
0.97
DEOGEN2
Benign
0.23
T;T;T;.
Eigen
Uncertain
0.32
Eigen_PC
Uncertain
0.34
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Benign
0.85
.;D;D;D
M_CAP
Pathogenic
0.66
D
MetaRNN
Pathogenic
0.81
D;D;D;D
MetaSVM
Uncertain
-0.16
T
MutationAssessor
Benign
1.4
L;L;.;.
PrimateAI
Pathogenic
0.90
D
PROVEAN
Uncertain
-4.3
.;D;D;.
REVEL
Pathogenic
0.68
Sift
Benign
0.12
.;T;T;.
Sift4G
Benign
0.19
.;T;T;.
Vest4
0.54, 0.54
MutPred
0.38
Gain of MoRF binding (P = 0.076);Gain of MoRF binding (P = 0.076);Gain of MoRF binding (P = 0.076);.;
MVP
0.54
ClinPred
0.99
D
GERP RS
4.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.52
gMVP
0.55

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-83208822; API