rs11933540

Positions:

• chr4-26118379-T-C

Variant summary

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

The XM_047415656.1(RBPJ):​c.-50+12601T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,058 control chromosomes in the GnomAD database, including 11,305 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 0.36 (11305 hom., cov: 32)
• Consequence: RBPJ XM_047415656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

Genes affected

RBPJ (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBPJ	XM_047415656.1	c.-50+12601T>C		intron_variant			XP_047271612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54124 AN: 151940 Hom.: 11270 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.356 AC: 54204 AN: 152058 Hom.: 11305 Cov.: 32 AF XY: 0.347 AC XY: 25819 AN XY: 74350

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.341

Alfa AF: 0.342 Hom.: 1269

Bravo AF: 0.366

Asia WGS AF: 0.0930 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11933540; hg19: chr4-26120001;