14-102592962-TCCGCCGCCG-TCCG

Variant names:

• chr14-102592962-TCCGCCG-T
• rs770589339
• NM_015156.4:c.85_90delGCCGCC

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3 BS2

The NM_015156.4(RCOR1):​c.85_90delGCCGCC​(p.Ala29_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 0.000153 in 1,166,106 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00043 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00011 (2 hom.)
• Consequence: RCOR1 NM_015156.4 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

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

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 63 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCOR1	NM_015156.4	c.85_90delGCCGCC	p.Ala29_Ala30del	conservative_inframe_deletion	Exon 1 of 12	ENST00000262241.7	NP_055971.2
RCOR1	XM_047431148.1	c.85_90delGCCGCC	p.Ala29_Ala30del	conservative_inframe_deletion	Exon 1 of 10		XP_047287104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RCOR1	ENST00000262241.7	c.85_90delGCCGCC	p.Ala29_Ala30del	conservative_inframe_deletion	Exon 1 of 12	1	NM_015156.4	ENSP00000262241.5

Frequencies

GnomAD3 genomes AF: 0.000436 AC: 64 AN: 146734 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000203

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000393

Gnomad SAS AF: 0.000418

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000106

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000225 AC: 5 AN: 22264 Hom.: 0 AF XY: 0.000289 AC XY: 4 AN XY: 13858

Gnomad AFR exome AF: 0.00368

Gnomad AMR exome AF: 0.000427

Gnomad ASJ exome AF: 0.000812

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000179

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000113 AC: 115 AN: 1019262 Hom.: 2 AF XY: 0.000106 AC XY: 52 AN XY: 491694

Gnomad4 AFR exome AF: 0.00111

Gnomad4 AMR exome AF: 0.000117

Gnomad4 ASJ exome AF: 0.000239

Gnomad4 EAS exome AF: 0.0000638

Gnomad4 SAS exome AF: 0.000336

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000777

Gnomad4 OTH exome AF: 0.000264

GnomAD4 genome AF: 0.000429 AC: 63 AN: 146844 Hom.: 0 Cov.: 32 AF XY: 0.000419 AC XY: 30 AN XY: 71626

Gnomad4 AFR AF: 0.00123

Gnomad4 AMR AF: 0.000135

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000395

Gnomad4 SAS AF: 0.000419

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000106

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs770589339; hg19: chr14-103059299;