Variant 14-102592979-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_015156.4(RCOR1):c.93C>T(p.Ser31Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0111 in 1,159,472 control chromosomes in the GnomAD database, including 96 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0080 ( 12 hom., cov: 33)

Exomes 𝑓: 0.012 ( 84 hom. )

Consequence

RCOR1
NM_015156.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.473

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 14-102592979-C-T is Benign according to our data. Variant chr14-102592979-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1588256.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.473 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0115 (11636/1011334) while in subpopulation MID AF= 0.0335 (84/2506). AF 95% confidence interval is 0.0277. There are 84 homozygotes in gnomad4_exome. There are 5644 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1182 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCOR1	NM_015156.4 link	c.93C>T	p.Ser31Ser	synonymous_variant	Exon 1 of 12	ENST00000262241.7	NP_055971.2	Q9UKL0
RCOR1	XM_047431148.1 link	c.93C>T	p.Ser31Ser	synonymous_variant	Exon 1 of 10		XP_047287104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RCOR1	ENST00000262241.7 link	c.93C>T	p.Ser31Ser	synonymous_variant	Exon 1 of 12	1	NM_015156.4	ENSP00000262241.5		Q9UKL0

Frequencies

GnomAD3 genomes

AF:

0.00799

AC:

1183

AN:

148030

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00195

Gnomad AMI

AF:

0.0319

Gnomad AMR

AF:

0.00751

Gnomad ASJ

AF:

0.0508

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.00645

Gnomad FIN

AF:

0.000327

Gnomad MID

AF:

0.0417

Gnomad NFE

AF:

0.0107

Gnomad OTH

AF:

0.0137

GnomAD3 exomes

AF:

0.0183

AC:

247

AN:

13462

Hom.:

AF XY:

0.0195

AC XY:

162

AN XY:

8320

show subpopulations

Gnomad AFR exome

AF:

0.00515

Gnomad AMR exome

AF:

0.00556

Gnomad ASJ exome

AF:

0.0709

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0108

Gnomad FIN exome

AF:

0.000572

Gnomad NFE exome

AF:

0.0196

Gnomad OTH exome

AF:

0.0171

GnomAD4 exome

AF:

0.0115

AC:

11636

AN:

1011334

Hom.:

Cov.:

AF XY:

0.0116

AC XY:

5644

AN XY:

486244

show subpopulations

Gnomad4 AFR exome

AF:

0.00184

Gnomad4 AMR exome

AF:

0.0101

Gnomad4 ASJ exome

AF:

0.0516

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00639

Gnomad4 FIN exome

AF:

0.00137

Gnomad4 NFE exome

AF:

0.0116

Gnomad4 OTH exome

AF:

0.0145

GnomAD4 genome

AF:

0.00798

AC:

1182

AN:

148138

Hom.:

Cov.:

AF XY:

0.00724

AC XY:

523

AN XY:

72230

show subpopulations

Gnomad4 AFR

AF:

0.00195

Gnomad4 AMR

AF:

0.00750

Gnomad4 ASJ

AF:

0.0508

Gnomad4 EAS

AF:

0.000195

Gnomad4 SAS

AF:

0.00687

Gnomad4 FIN

AF:

0.000327

Gnomad4 NFE

AF:

0.0107

Gnomad4 OTH

AF:

0.0131

Alfa

AF:

0.00186

Hom.:

Bravo

AF:

0.00843

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jan 20, 2025

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

BayesDel_noAF

Benign

-0.70

CADD

Benign

8.1

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.6

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