dbSNP rs3213716: RPS6KL1:c.532-102C>T (chr14-74911482-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031464.5(RPS6KL1):c.532-102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,356,996 control chromosomes in the GnomAD database, including 101,146 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.30 ( 8714 hom., cov: 31)

Exomes 𝑓: 0.39 ( 92432 hom. )

Consequence

RPS6KL1
NM_031464.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.711

Publications

12 publications found

Variant links:

Genes affected

RPS6KL1 (HGNC:20222): (ribosomal protein S6 kinase like 1) Predicted to enable ATP binding activity; protein serine kinase activity; and protein serine/threonine kinase activity. Predicted to be involved in protein phosphorylation. Predicted to be located in ribosome. [provided by Alliance of Genome Resources, Apr 2022]

RPS6KL1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPS6KL1	NM_031464.5 link	c.532-102C>T		intron_variant	Intron 6 of 11	ENST00000557413.6	NP_113652.2	Q9Y6S9-1B4DSP6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS6KL1	ENST00000557413.6 link	c.532-102C>T		intron_variant	Intron 6 of 11	5	NM_031464.5	ENSP00000450567.1		Q9Y6S9-1

Frequencies

GnomAD3 genomes

AF:

0.305

AC:

46288

AN:

151916

Hom.:

8714

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0808

Gnomad AMI

AF:

0.320

Gnomad AMR

AF:

0.424

Gnomad ASJ

AF:

0.423

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.279

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.376

Gnomad NFE

AF:

0.396

Gnomad OTH

AF:

0.341

GnomAD4 exome

AF:

0.385

AC:

464214

AN:

1204962

Hom.:

92432

Cov.:

AF XY:

0.383

AC XY:

229019

AN XY:

598358

show subpopulations

African (AFR)

AF:

0.0647

AC:

1834

AN:

28332

American (AMR)

AF:

0.481

AC:

17740

AN:

36896

Ashkenazi Jewish (ASJ)

AF:

0.431

AC:

8994

AN:

20872

East Asian (EAS)

AF:

0.511

AC:

19295

AN:

37724

South Asian (SAS)

AF:

0.294

AC:

21242

AN:

72176

European-Finnish (FIN)

AF:

0.285

AC:

10048

AN:

35232

Middle Eastern (MID)

AF:

0.383

AC:

1381

AN:

3608

European-Non Finnish (NFE)

AF:

0.396

AC:

363909

AN:

918808

Other (OTH)

AF:

0.385

AC:

19771

AN:

51314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

14359

28718

43077

57436

71795

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.304

AC:

46291

AN:

152034

Hom.:

8714

Cov.:

AF XY:

0.302

AC XY:

22473

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.0805

AC:

3341

AN:

41506

American (AMR)

AF:

0.424

AC:

6482

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.423

AC:

1467

AN:

3472

East Asian (EAS)

AF:

0.552

AC:

2838

AN:

5140

South Asian (SAS)

AF:

0.279

AC:

1347

AN:

4822

European-Finnish (FIN)

AF:

0.266

AC:

2822

AN:

10596

Middle Eastern (MID)

AF:

0.377

AC:

110

AN:

292

European-Non Finnish (NFE)

AF:

0.396

AC:

26874

AN:

67904

Other (OTH)

AF:

0.341

AC:

718

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1489

2978

4467

5956

7445

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.344

Hom.:

1577

Bravo

AF:

0.311

Asia WGS

AF:

0.363

AC:

1263

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.36

(source)

DANN

Benign

0.63

PhyloP100

-0.71

PromoterAI

-0.026

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs3213716

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over