Menu
GeneBe

17-38850487-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_000978.4(RPL23):c.227-12T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000415 in 1,590,452 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 0.00048 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00041 ( 2 hom. )

Consequence

RPL23
NM_000978.4 splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.0001050
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.478
Variant links:
Genes affected
RPL23 (HGNC:10316): (ribosomal protein L23) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L14P family of ribosomal proteins. It is located in the cytoplasm. This gene has been referred to as rpL17 because the encoded protein shares amino acid identity with ribosomal protein L17 from Saccharomyces cerevisiae; however, its official symbol is RPL23. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 17-38850487-A-G is Benign according to our data. Variant chr17-38850487-A-G is described in ClinVar as [Benign]. Clinvar id is 1972183.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd at 73 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL23NM_000978.4 linkuse as main transcriptc.227-12T>C splice_polypyrimidine_tract_variant, intron_variant ENST00000479035.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL23ENST00000479035.7 linkuse as main transcriptc.227-12T>C splice_polypyrimidine_tract_variant, intron_variant 1 NM_000978.4 P1

Frequencies

GnomAD3 genomes
AF:
0.000480
AC:
73
AN:
152202
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00462
Gnomad SAS
AF:
0.000828
Gnomad FIN
AF:
0.00282
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.000959
GnomAD3 exomes
AF:
0.000964
AC:
241
AN:
249984
Hom.:
0
AF XY:
0.000858
AC XY:
116
AN XY:
135140
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000586
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00507
Gnomad SAS exome
AF:
0.000231
Gnomad FIN exome
AF:
0.00509
Gnomad NFE exome
AF:
0.000230
Gnomad OTH exome
AF:
0.000492
GnomAD4 exome
AF:
0.000408
AC:
587
AN:
1438132
Hom.:
2
Cov.:
26
AF XY:
0.000399
AC XY:
286
AN XY:
717086
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000450
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00407
Gnomad4 SAS exome
AF:
0.000117
Gnomad4 FIN exome
AF:
0.00466
Gnomad4 NFE exome
AF:
0.000120
Gnomad4 OTH exome
AF:
0.000571
GnomAD4 genome
AF:
0.000479
AC:
73
AN:
152320
Hom.:
0
Cov.:
32
AF XY:
0.000685
AC XY:
51
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00463
Gnomad4 SAS
AF:
0.000829
Gnomad4 FIN
AF:
0.00282
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.000949
Alfa
AF:
0.000215
Hom.:
0
Bravo
AF:
0.000253
Asia WGS
AF:
0.00549
AC:
19
AN:
3478

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 testingInvitaeJan 25, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
3.6
Dann
Benign
0.68
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.3

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00011
dbscSNV1_RF
Benign
0.038
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: rs138762930; hg19: chr17-37006740; API