Variant rs753306232 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_016120.4(RLIM):c.-23-12_-23-11del 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 0.00108 in 1,040,001 control chromosomes in the GnomAD database, including 1 homozygotes. There are 387 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00089 ( 0 hom., 41 hem., cov: 23)

Exomes 𝑓: 0.0011 ( 1 hom. 346 hem. )

Consequence

RLIM
NM_016120.4 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.85

Variant links:

Genes affected

RLIM (HGNC:13429): (ring finger protein, LIM domain interacting) The protein encoded by this gene is a RING-H2 zinc finger protein. It has been shown to be an E3 ubiquitin protein ligase that targets LIM domain binding 1 (LDB1/CLIM), and causes proteasome-dependent degradation of LDB1. This protein and LDB1 are co-repressors of LHX1/LIM-1, a homeodomain transcription factor. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Feb 2009]

RLIM links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant X-74596010-GAA-G is Benign according to our data. Variant chrX-74596010-GAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 446076.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 41 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RLIM	NM_016120.4 linkuse as main transcript	c.-23-12_-23-11del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000332687.11
RLIM	NM_183353.3 linkuse as main transcript	c.-23-12_-23-11del		splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RLIM	ENST00000332687.11 linkuse as main transcript	c.-23-12_-23-11del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_016120.4	P1	Q9NVW2-1
RLIM	ENST00000349225.2 linkuse as main transcript	c.-23-12_-23-11del		splice_polypyrimidine_tract_variant, intron_variant		2		P1	Q9NVW2-1

Frequencies

GnomAD3 genomes

AF:

0.000881

AC:

AN:

112413

Hom.:

Cov.:

AF XY:

0.00115

AC XY:

AN XY:

34639

show subpopulations

Gnomad AFR

AF:

0.0000969

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000564

Gnomad ASJ

AF:

0.00113

Gnomad EAS

AF:

0.00278

Gnomad SAS

AF:

0.00292

Gnomad FIN

AF:

0.00424

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000770

Gnomad OTH

AF:

0.00133

GnomAD3 exomes

AF:

0.00147

AC:

195

AN:

132280

Hom.:

AF XY:

0.00219

AC XY:

AN XY:

36576

show subpopulations

Gnomad AFR exome

AF:

0.0000909

Gnomad AMR exome

AF:

0.000262

Gnomad ASJ exome

AF:

0.000880

Gnomad EAS exome

AF:

0.00263

Gnomad SAS exome

AF:

0.00348

Gnomad FIN exome

AF:

0.00348

Gnomad NFE exome

AF:

0.00101

Gnomad OTH exome

AF:

0.00342

GnomAD4 exome

AF:

0.00110

AC:

1020

AN:

927538

Hom.:

AF XY:

0.00144

AC XY:

346

AN XY:

240350

show subpopulations

Gnomad4 AFR exome

AF:

0.000138

Gnomad4 AMR exome

AF:

0.000338

Gnomad4 ASJ exome

AF:

0.00150

Gnomad4 EAS exome

AF:

0.000708

Gnomad4 SAS exome

AF:

0.00391

Gnomad4 FIN exome

AF:

0.00272

Gnomad4 NFE exome

AF:

0.000914

Gnomad4 OTH exome

AF:

0.00149

GnomAD4 genome

AF:

0.000889

AC:

100

AN:

112463

Hom.:

Cov.:

AF XY:

0.00118

AC XY:

AN XY:

34699

show subpopulations

Gnomad4 AFR

AF:

0.0000967

Gnomad4 AMR

AF:

0.000564

Gnomad4 ASJ

AF:

0.00113

Gnomad4 EAS

AF:

0.00278

Gnomad4 SAS

AF:

0.00330

Gnomad4 FIN

AF:

0.00424

Gnomad4 NFE

AF:

0.000770

Gnomad4 OTH

AF:

0.00132

Alfa

AF:

0.000498

Hom.:

Bravo

AF:

0.000567

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

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Feb 24, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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