NM_015156.4:c.76_81dupTCCGCC

Variant names:

• chr14-102592950-G-GCCGCCT
• rs747961008
• NM_015156.4:c.76_81dupTCCGCC

Variant summary

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

The NM_015156.4(RCOR1):​c.76_81dupTCCGCC​(p.Ser26_Ala27dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,189,376 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 0.00018 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000095 (0 hom.)
• Consequence: RCOR1 NM_015156.4 conservative_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

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 26 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCOR1	NM_015156.4	c.76_81dupTCCGCC	p.Ser26_Ala27dup	conservative_inframe_insertion	Exon 1 of 12	ENST00000262241.7	NP_055971.2
RCOR1	XM_047431148.1	c.76_81dupTCCGCC	p.Ser26_Ala27dup	conservative_inframe_insertion	Exon 1 of 10		XP_047287104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RCOR1	ENST00000262241.7	c.76_81dupTCCGCC	p.Ser26_Ala27dup	conservative_inframe_insertion	Exon 1 of 12	1	NM_015156.4	ENSP00000262241.5

Frequencies

GnomAD3 genomes AF: 0.000176 AC: 26 AN: 148048 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000488

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000402

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00175

Gnomad SAS AF: 0.000209

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000121

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000121 AC: 4 AN: 33168 Hom.: 0 AF XY: 0.0000488 AC XY: 1 AN XY: 20480

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000481

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000951 AC: 99 AN: 1041220 Hom.: 0 Cov.: 33 AF XY: 0.0000952 AC XY: 48 AN XY: 503948

Gnomad4 AFR exome AF: 0.0000491

Gnomad4 AMR exome AF: 0.000202

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000901

Gnomad4 SAS exome AF: 0.000517

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000563

Gnomad4 OTH exome AF: 0.000361

GnomAD4 genome AF: 0.000175 AC: 26 AN: 148156 Hom.: 0 Cov.: 33 AF XY: 0.000166 AC XY: 12 AN XY: 72316

Gnomad4 AFR AF: 0.0000487

Gnomad4 AMR AF: 0.000401

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00175

Gnomad4 SAS AF: 0.000209

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000121

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: rs747961008; hg19: chr14-103059287;