NM_015156.4:c.82_90delGCCGCCGCC

Variant names:

• chr14-102592962-TCCGCCGCCG-T
• rs770589339
• NM_015156.4:c.82_90delGCCGCCGCC

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3 BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_015156.4
• BS2: High AC in GnomAd4 at 6 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015156.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RCOR1	NM_015156.4	MANE Select	c.82_90delGCCGCCGCC	p.Ala28_Ala30del	conservative_inframe_deletion	Exon 1 of 12	NP_055971.2	Q9UKL0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RCOR1	ENST00000262241.7	TSL:1 MANE Select	c.82_90delGCCGCCGCC	p.Ala28_Ala30del	conservative_inframe_deletion	Exon 1 of 12	ENSP00000262241.5	Q9UKL0
	RCOR1	ENST00000908570.1		c.82_90delGCCGCCGCC	p.Ala28_Ala30del	conservative_inframe_deletion	Exon 1 of 12	ENSP00000578629.1

Frequencies

GnomAD3 genomes AF: 0.0000409 AC: 6 AN: 146734 Hom.: 0 Cov.: 32

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

African (AFR) AF: 0.00 AC: 0 AN: 19844

American (AMR) AF: 0.000117 AC: 1 AN: 8576

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12538

East Asian (EAS) AF: 0.000128 AC: 2 AN: 15662

South Asian (SAS) AF: 0.00 AC: 0 AN: 29810

European-Finnish (FIN) AF: 0.0000592 AC: 1 AN: 16890

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2562

European-Non Finnish (NFE) AF: 0.0000251 AC: 22 AN: 875578

Other (OTH) AF: 0.00 AC: 0 AN: 37808

GnomAD4 genome AF: 0.0000409 AC: 6 AN: 146844 Hom.: 0 Cov.: 32 AF XY: 0.0000279 AC XY: 2 AN XY: 71626

African (AFR) AF: 0.00 AC: 0 AN: 40632

American (AMR) AF: 0.00 AC: 0 AN: 14826

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3384

East Asian (EAS) AF: 0.000395 AC: 2 AN: 5068

South Asian (SAS) AF: 0.00 AC: 0 AN: 4776

European-Finnish (FIN) AF: 0.000109 AC: 1 AN: 9156

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.0000456 AC: 3 AN: 65764

Other (OTH) AF: 0.00 AC: 0 AN: 2044

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.5
Mutation Taster		=171/29	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs770589339; hg19: chr14-103059299; COSMIC: COSV104572346;