Variant 14-102592956-TCCGCCTCCGCCGCCG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_015156.4(RCOR1):c.88_102delGCCTCCGCCGCCGCC(p.Ala30_Ala34del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000313 in 1,174,254 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00034 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00031 ( 0 hom. )

Consequence

RCOR1
NM_015156.4 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.27

Variant links:

Genes affected

RCOR1 (HGNC:17441): (REST corepressor 1) This gene encodes a protein that is well-conserved, downregulated at birth, and with a specific role in determining neural cell differentiation. The encoded protein binds to the C-terminal domain of REST (repressor element-1 silencing transcription factor). [provided by RefSeq, Aug 2011]

RCOR1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_015156.4

BS2

High AC in GnomAd4 at 50 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RCOR1	NM_015156.4 linkuse as main transcript	c.88_102delGCCTCCGCCGCCGCC	p.Ala30_Ala34del	conservative_inframe_deletion	1/12	ENST00000262241.7	NP_055971.2	Q9UKL0
RCOR1	XM_047431148.1 linkuse as main transcript	c.88_102delGCCTCCGCCGCCGCC	p.Ala30_Ala34del	conservative_inframe_deletion	1/10		XP_047287104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RCOR1	ENST00000262241.7 linkuse as main transcript	c.88_102delGCCTCCGCCGCCGCC	p.Ala30_Ala34del	conservative_inframe_deletion	1/12	1	NM_015156.4	ENSP00000262241.5		Q9UKL0

Frequencies

GnomAD3 genomes

AF:

0.000341

AC:

AN:

146820

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000272

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000672

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000211

Gnomad FIN

AF:

0.000109

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000395

Gnomad OTH

AF:

0.000495

GnomAD3 exomes

AF:

0.000183

AC:

AN:

27292

Hom.:

AF XY:

0.000237

AC XY:

AN XY:

16892

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000684

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000146

Gnomad FIN exome

AF:

0.000393

Gnomad NFE exome

AF:

0.0000949

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000310

AC:

318

AN:

1027324

Hom.:

AF XY:

0.000302

AC XY:

150

AN XY:

496340

show subpopulations

Gnomad4 AFR exome

AF:

0.000350

Gnomad4 AMR exome

AF:

0.000226

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000562

Gnomad4 SAS exome

AF:

0.000613

Gnomad4 FIN exome

AF:

0.000233

Gnomad4 NFE exome

AF:

0.000299

Gnomad4 OTH exome

AF:

0.000340

GnomAD4 genome

AF:

0.000340

AC:

AN:

146930

Hom.:

Cov.:

AF XY:

0.000335

AC XY:

AN XY:

71658

show subpopulations

Gnomad4 AFR

AF:

0.000271

Gnomad4 AMR

AF:

0.000671

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000211

Gnomad4 FIN

AF:

0.000109

Gnomad4 NFE

AF:

0.000395

Gnomad4 OTH

AF:

0.000488

Bravo

AF:

0.000314

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Apr 30, 2023

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with RCOR1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant, c.88_102del, results in the deletion of 5 amino acid(s) of the RCOR1 protein (p.Ala30_Ala34del), but otherwise preserves the integrity of the reading frame. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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