Genetic Variant RPS15A:c.214-12_214-10delGTT (chr16-18784832-TAAC-T) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001019.5(RPS15A):c.214-12_214-10delGTT variant causes a 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 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]

RPS15A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -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 GnomAd4 at 24 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPS15A	NM_001019.5 link	c.214-12_214-10delGTT		intron_variant	Intron 3 of 4	ENST00000322989.8	NP_001010.2	P62244B2R4W8
RPS15A	NM_001030009.2 link	c.214-12_214-10delGTT		intron_variant	Intron 3 of 4		NP_001025180.1	P62244B2R4W8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS15A	ENST00000322989.8 link	c.214-12_214-10delGTT		intron_variant	Intron 3 of 4	1	NM_001019.5	ENSP00000318646.4		P62244

Frequencies

GnomAD3 genomes

AF:

0.000158

AC:

AN:

152034

Hom.:

Cov.:

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

GnomAD2 exomes

AF:

0.000220

AC:

AN:

231822

AF XY:

0.000183

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 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.:

AF XY:

0.000174

AC XY:

124

AN XY:

713444

show subpopulations

Gnomad4 AFR exome

AF:

0.000187

AC:

AN:

32100

Gnomad4 AMR exome

AF:

0.000230

AC:

AN:

39092

Gnomad4 ASJ exome

AF:

0.000356

AC:

AN:

25300

Gnomad4 EAS exome

AF:

0.00249

AC:

AN:

39406

Gnomad4 SAS exome

AF:

0.0000244

AC:

AN:

82030

Gnomad4 FIN exome

AF:

0.00

AC:

AN:

53232

Gnomad4 NFE exome

AF:

0.000118

AC:

129

AN:

1096978

Gnomad4 Remaining exome

AF:

0.000118

AC:

AN:

59354

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000158

AC:

AN:

152152

Hom.:

Cov.:

AF XY:

0.000229

AC XY:

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.0000723

AC:

0.0000722613

AN:

0.0000722613

Gnomad4 AMR

AF:

0.000458

AC:

0.000457875

AN:

0.000457875

Gnomad4 ASJ

AF:

0.000865

AC:

0.000864553

AN:

0.000864553

Gnomad4 EAS

AF:

0.000966

AC:

0.000965624

AN:

0.000965624

Gnomad4 SAS

AF:

0.000208

AC:

0.000207555

AN:

0.000207555

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.0000736

AC:

0.0000735597

AN:

0.0000735597

Gnomad4 OTH

AF:

0.00

AC:

AN:

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000182

Hom.:

Bravo

AF:

0.000223

Asia WGS

AF:

0.000289

AC:

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

Dec 19, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=100/0

polymorphism

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