Variant chr15-82538226-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001021.6(RPS17):c.327+80G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,502,318 control chromosomes in the GnomAD database, including 971 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 102 hom., cov: 32)

Exomes 𝑓: 0.010 ( 869 hom. )

Consequence

RPS17
NM_001021.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.94

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]

RPS17 links:

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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 (MetaRNN=0.0052820444).

BP6

Variant 15-82538226-C-T is Benign according to our data. Variant chr15-82538226-C-T is described in ClinVar as [Benign]. Clinvar id is 1686316.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
RPS17	NM_001021.6 linkuse as main transcript	c.327+80G>A	intron_variant	ENST00000647841.1
RPS17	NR_111943.2 linkuse as main transcript	n.649+80G>A	intron_variant, non_coding_transcript_variant
RPS17	NR_111944.3 linkuse as main transcript	n.356+80G>A	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS17	ENST00000647841.1 linkuse as main transcript	c.327+80G>A		intron_variant			NM_001021.6	P1

Frequencies

GnomAD3 genomes

AF:

0.0157

AC:

2389

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00304

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0742

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.121

Gnomad SAS

AF:

0.00621

Gnomad FIN

AF:

0.0332

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00129

Gnomad OTH

AF:

0.0124

GnomAD4 exome

AF:

0.0103

AC:

13905

AN:

1350034

Hom.:

869

Cov.:

AF XY:

0.00931

AC XY:

6312

AN XY:

677774

show subpopulations

Gnomad4 AFR exome

AF:

0.00174

Gnomad4 AMR exome

AF:

0.154

Gnomad4 ASJ exome

AF:

0.000396

Gnomad4 EAS exome

AF:

0.0983

Gnomad4 SAS exome

AF:

0.00408

Gnomad4 FIN exome

AF:

0.0288

Gnomad4 NFE exome

AF:

0.000696

Gnomad4 OTH exome

AF:

0.0114

GnomAD4 genome

AF:

0.0158

AC:

2407

AN:

152284

Hom.:

102

Cov.:

AF XY:

0.0183

AC XY:

1361

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.00303

Gnomad4 AMR

AF:

0.0753

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.122

Gnomad4 SAS

AF:

0.00643

Gnomad4 FIN

AF:

0.0332

Gnomad4 NFE

AF:

0.00129

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.0102

Hom.:

Bravo

AF:

0.0218

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 submitter

clinical testing

Mendelics

May 04, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Benign

-0.59

CADD

Benign

0.33

DANN

Benign

0.79

DEOGEN2

Benign

0.0059

FATHMM_MKL

Benign

0.0020

LIST_S2

Benign

0.22

M_CAP

Uncertain

0.15

MetaRNN

Benign

0.0053

MutationTaster

Benign

1.0

N;N

PROVEAN

Benign

0.24

Sift

Benign

0.086

Vest4

0.13

MVP

0.12

GERP RS

-0.41

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over