rs770589339

Variant summary

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

The NM_015156.4(RCOR1):​c.82_90delGCCGCCGCC​(p.Ala28_Ala30del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,166,112 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000041 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000026 ( 0 hom. )

Consequence

RCOR1
NM_015156.4 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.51
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]

Genome browser will be placed here

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 6 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RCOR1NM_015156.4 linkc.82_90delGCCGCCGCC p.Ala28_Ala30del conservative_inframe_deletion Exon 1 of 12 ENST00000262241.7 NP_055971.2 Q9UKL0
RCOR1XM_047431148.1 linkc.82_90delGCCGCCGCC p.Ala28_Ala30del conservative_inframe_deletion Exon 1 of 10 XP_047287104.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RCOR1ENST00000262241.7 linkc.82_90delGCCGCCGCC p.Ala28_Ala30del conservative_inframe_deletion Exon 1 of 12 1 NM_015156.4 ENSP00000262241.5 Q9UKL0

Frequencies

GnomAD3 genomes
AF:
0.0000409
AC:
6
AN:
146734
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000393
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000109
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000456
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000255
AC:
26
AN:
1019268
Hom.:
0
AF XY:
0.0000264
AC XY:
13
AN XY:
491696
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000117
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000128
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000592
Gnomad4 NFE exome
AF:
0.0000251
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000409
AC:
6
AN:
146844
Hom.:
0
Cov.:
32
AF XY:
0.0000279
AC XY:
2
AN XY:
71626
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000395
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000109
Gnomad4 NFE
AF:
0.0000456
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000302

ClinVar

Not reported in ClinVar

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.

Other links and lift over

dbSNP: rs770589339; hg19: chr14-103059299; API