Genetic Variant NM_015156.4:c.96_97insTCCGCCGCCGCCGCCTCCGCCTCCGCCGCCGCCGCCTCCGCC (chr14-102592949-G-GGCCGCCTCCGCCTCCGCCGCCGCCGCCTCCGCCTCCGCCGCC) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3

The NM_015156.4(RCOR1):c.96_97insTCCGCCGCCGCCGCCTCCGCCTCCGCCGCCGCCGCCTCCGCC(p.Ala32_Ala33insSerAlaAlaAlaAlaSerAlaSerAlaAlaAlaAlaSerAla) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000673 in 148,660 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 0.0000067 ( 0 hom., cov: 33)

Consequence

RCOR1
NM_015156.4 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.983

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]

RCOR1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP3

Nonframeshift variant in repetitive region in NM_015156.4

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCOR1	NM_015156.4 link	c.96_97insTCCGCCGCCGCCGCCTCCGCCTCCGCCGCCGCCGCCTCCGCC	p.Ala32_Ala33insSerAlaAlaAlaAlaSerAlaSerAlaAlaAlaAlaSerAla	conservative_inframe_insertion	Exon 1 of 12	ENST00000262241.7	NP_055971.2	Q9UKL0
RCOR1	XM_047431148.1 link	c.96_97insTCCGCCGCCGCCGCCTCCGCCTCCGCCGCCGCCGCCTCCGCC	p.Ala32_Ala33insSerAlaAlaAlaAlaSerAlaSerAlaAlaAlaAlaSerAla	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 link	c.96_97insTCCGCCGCCGCCGCCTCCGCCTCCGCCGCCGCCGCCTCCGCC	p.Ala32_Ala33insSerAlaAlaAlaAlaSerAlaSerAlaAlaAlaAlaSerAla	conservative_inframe_insertion	Exon 1 of 12	1	NM_015156.4	ENSP00000262241.5		Q9UKL0

Frequencies

GnomAD3 genomes

AF:

0.00000673

AC:

AN:

148660

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000244

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

AF:

0.00000673

AC:

AN:

148660

Hom.:

Cov.:

AF XY:

0.0000138

AC XY:

AN XY:

72452

show subpopulations

Gnomad4 AFR

AF:

0.0000244

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over