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16-18784832-TAAC-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001019.5(RPS15A):c.214-12_214-10del 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 0.000182 in 1,585,296 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00018 ( 1 hom. )

Consequence

RPS15A
NM_001019.5 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.303
Variant links:
Genes affected
RPS15A (HGNC:10389): (ribosomal protein S15a) 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 40S subunit. The protein belongs to the S8P family of ribosomal proteins. It is located in the cytoplasm. 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 Likely_benign. Variant got -6 ACMG points.

BP6
Variant 16-18784832-TAAC-T is Benign according to our data. Variant chr16-18784832-TAAC-T is described in ClinVar as [Likely_benign]. Clinvar id is 2746992.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd at 24 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS15ANM_001019.5 linkuse as main transcriptc.214-12_214-10del splice_polypyrimidine_tract_variant, intron_variant ENST00000322989.8
RPS15ANM_001030009.2 linkuse as main transcriptc.214-12_214-10del splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS15AENST00000322989.8 linkuse as main transcriptc.214-12_214-10del splice_polypyrimidine_tract_variant, intron_variant 1 NM_001019.5 P1

Frequencies

GnomAD3 genomes
AF:
0.000158
AC:
24
AN:
152034
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.000865
Gnomad EAS
AF:
0.000963
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000736
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000220
AC:
51
AN:
231822
Hom.:
1
AF XY:
0.000183
AC XY:
23
AN XY:
125518
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000246
Gnomad ASJ exome
AF:
0.000443
Gnomad EAS exome
AF:
0.00105
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000184
Gnomad OTH exome
AF:
0.000352
GnomAD4 exome
AF:
0.000184
AC:
264
AN:
1433144
Hom.:
1
AF XY:
0.000174
AC XY:
124
AN XY:
713444
show subpopulations
Gnomad4 AFR exome
AF:
0.000187
Gnomad4 AMR exome
AF:
0.000230
Gnomad4 ASJ exome
AF:
0.000356
Gnomad4 EAS exome
AF:
0.00249
Gnomad4 SAS exome
AF:
0.0000244
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000118
Gnomad4 OTH exome
AF:
0.000118
GnomAD4 genome
AF:
0.000158
AC:
24
AN:
152152
Hom.:
0
Cov.:
32
AF XY:
0.000229
AC XY:
17
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0000723
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.000865
Gnomad4 EAS
AF:
0.000966
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000736
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000182
Hom.:
0
Bravo
AF:
0.000223
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.000274
EpiControl
AF:
0.000179

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeOct 20, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs762572023; hg19: chr16-18796154; API