20-45316318-G-C

Variant names:

• chr20-45316318-G-C
• NM_014276.4:c.1152G>C
• RBPJL p.Pro384Pro

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_014276.4(RBPJL):​c.1152G>C​(p.Pro384Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: RBPJL NM_014276.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.96
• Publications: 0 publications found

Genes affected

RBPJL (HGNC:13761): (recombination signal binding protein for immunoglobulin kappa J region like) This gene encodes a member of the suppressor of hairless protein family. A similar protein in mouse is a transcription factor that binds to DNA sequences almost identical to that bound by the Notch receptor signaling pathway transcription factor recombining binding protein J. The mouse protein has been shown to activate transcription in concert with Epstein-Barr virus nuclear antigen-2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP7: Synonymous conserved (PhyloP=-5.96 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014276.4. 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
	RBPJL	NM_014276.4	MANE Select	c.1152G>C	p.Pro384Pro	synonymous	Exon 10 of 12	NP_055091.2
	RBPJL	NM_001281449.2		c.1152G>C	p.Pro384Pro	synonymous	Exon 10 of 12	NP_001268378.1	Q9UBG7-2
	RBPJL	NM_001281448.2		c.1152G>C	p.Pro384Pro	synonymous	Exon 10 of 12	NP_001268377.1	Q5QPV1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBPJL	ENST00000343694.8	TSL:1 MANE Select	c.1152G>C	p.Pro384Pro	synonymous	Exon 10 of 12	ENSP00000341243.3	Q9UBG7-1
	RBPJL	ENST00000372743.5	TSL:1	c.1152G>C	p.Pro384Pro	synonymous	Exon 10 of 12	ENSP00000361828.1	Q9UBG7-2
	RBPJL	ENST00000372741.7	TSL:1	c.1152G>C	p.Pro384Pro	synonymous	Exon 10 of 12	ENSP00000361826.3	Q5QPV1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.55
DANN	Benign	0.56
PhyloP100		-6.0

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr20-43944958;