Variant chr16-11847661-T-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000571133.6(RSL1D1):c.384+7A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 1,604,056 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0044 ( 26 hom. )

Consequence

RSL1D1
ENST00000571133.6 splice_region, intron

Scores

Splicing: ADA: 0.0001635

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.355

Variant links:

Genes affected

RSL1D1 (HGNC:24534): (ribosomal L1 domain containing 1) Enables mRNA 3'-UTR binding activity and mRNA 5'-UTR binding activity. Involved in regulation of apoptotic process and regulation of cellular senescence. Acts upstream of or within regulation of protein localization. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

RSL1D1 links:

RSL1D1 (HGNC:):

RSL1D1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 16-11847661-T-A is Benign according to our data. Variant chr16-11847661-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2646231.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 26 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSL1D1	NM_015659.3 linkuse as main transcript	c.384+7A>T		splice_region_variant, intron_variant		ENST00000571133.6	NP_056474.2	O76021-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSL1D1	ENST00000571133.6 linkuse as main transcript	c.384+7A>T		splice_region_variant, intron_variant		1	NM_015659.3	ENSP00000460871.1		O76021-1

Frequencies

GnomAD3 genomes

AF:

0.00280

AC:

427

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000965

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00196

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00951

Gnomad FIN

AF:

0.000941

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00404

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00383

AC:

941

AN:

245550

Hom.:

AF XY:

0.00442

AC XY:

587

AN XY:

132892

show subpopulations

Gnomad AFR exome

AF:

0.000868

Gnomad AMR exome

AF:

0.00148

Gnomad ASJ exome

AF:

0.00234

Gnomad EAS exome

AF:

0.000110

Gnomad SAS exome

AF:

0.00908

Gnomad FIN exome

AF:

0.00121

Gnomad NFE exome

AF:

0.00472

Gnomad OTH exome

AF:

0.00548

GnomAD4 exome

AF:

0.00436

AC:

6330

AN:

1451694

Hom.:

Cov.:

AF XY:

0.00461

AC XY:

3327

AN XY:

721932

show subpopulations

Gnomad4 AFR exome

AF:

0.00137

Gnomad4 AMR exome

AF:

0.00173

Gnomad4 ASJ exome

AF:

0.00274

Gnomad4 EAS exome

AF:

0.0000506

Gnomad4 SAS exome

AF:

0.00964

Gnomad4 FIN exome

AF:

0.00143

Gnomad4 NFE exome

AF:

0.00446

Gnomad4 OTH exome

AF:

0.00438

GnomAD4 genome

AF:

0.00281

AC:

428

AN:

152362

Hom.:

Cov.:

AF XY:

0.00287

AC XY:

214

AN XY:

74506

show subpopulations

Gnomad4 AFR

AF:

0.000962

Gnomad4 AMR

AF:

0.00196

Gnomad4 ASJ

AF:

0.00403

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00972

Gnomad4 FIN

AF:

0.000941

Gnomad4 NFE

AF:

0.00404

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00384

Hom.:

Bravo

AF:

0.00277

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.00496

EpiControl

AF:

0.00445

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2023

RSL1D1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

1.3

DANN

Benign

0.79

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00016

dbscSNV1_RF

Benign

0.0020

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