rs714827

Positions:

• chr14-102647215-G-A
• chr14-102647215-G-C
• chr14-102647215-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015156.4(RCOR1):​c.362-34680G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,324 control chromosomes in the GnomAD database, including 67,609 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.94 (67609 hom., cov: 32)
• Consequence: RCOR1 NM_015156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RCOR1	NM_015156.4	c.362-34680G>A		intron_variant		ENST00000262241.7
RCOR1	XM_047431148.1	c.362-34680G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RCOR1	ENST00000262241.7	c.362-34680G>A		intron_variant		1	NM_015156.4	P1

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143258 AN: 152206 Hom.: 67551 Cov.: 32

Gnomad AFR AF: 0.985

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.952

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.941 AC: 143375 AN: 152324 Hom.: 67609 Cov.: 32 AF XY: 0.939 AC XY: 69962 AN XY: 74482

Gnomad4 AFR AF: 0.985

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.925

Gnomad4 OTH AF: 0.953

Alfa AF: 0.930 Hom.: 34659

Bravo AF: 0.944

Asia WGS AF: 0.981 AC: 3412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs714827; hg19: chr14-103113552;