14-102593037-GCCT-GCCTCCT

Variant names:

• chr14-102593037-G-GCCT
• rs908905035
• NM_015156.4:c.156_158dupCTC

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_015156.4(RCOR1):​c.156_158dupCTC​(p.Ser53dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000877 in 1,140,490 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: not found (cov: 33)
  • Exomes 𝑓: 8.8e-7 (0 hom.)
• Consequence: RCOR1 NM_015156.4 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.156_158dupCTC	p.Ser53dup	disruptive_inframe_insertion	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.156_158dupCTC	p.Ser53dup	disruptive_inframe_insertion	Exon 1 of 12	ENSP00000262241.5	Q9UKL0
	RCOR1	ENST00000908570.1		c.156_158dupCTC	p.Ser53dup	disruptive_inframe_insertion	Exon 1 of 12	ENSP00000578629.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 8.77e-7 AC: 1 AN: 1140490 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 553934

African (AFR) AF: 0.00 AC: 0 AN: 22388

American (AMR) AF: 0.00 AC: 0 AN: 10858

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16712

East Asian (EAS) AF: 0.00 AC: 0 AN: 25124

South Asian (SAS) AF: 0.00 AC: 0 AN: 38314

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36082

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3082

European-Non Finnish (NFE) AF: 0.00000106 AC: 1 AN: 943396

Other (OTH) AF: 0.00 AC: 0 AN: 44534

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs908905035; hg19: chr14-103059374;