5-160253612-C-G

Variant names:

• chr5-160253612-C-G
• NM_001308173.3:c.930G>C
• CCNJL p.Arg310Arg

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001308173.3(CCNJL):​c.930G>C​(p.Arg310Arg) 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: CCNJL NM_001308173.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.931
• Publications: 0 publications found

Genes affected

CCNJL (HGNC:25876): (cyclin J like) Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be involved in mitotic cell cycle phase transition and regulation of cyclin-dependent protein serine/threonine kinase activity. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Predicted to be active in centrosome; cytoplasm; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BP7: Synonymous conserved (PhyloP=0.931 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001308173.3. 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
	CCNJL	NM_001308173.3	MANE Select	c.930G>C	p.Arg310Arg	synonymous	Exon 6 of 6	NP_001295102.1	B4DZA8
	CCNJL	NM_024565.8		c.1074G>C	p.Arg358Arg	synonymous	Exon 7 of 7	NP_078841.3
	CCNJL	NR_131769.2		n.1403G>C		non_coding_transcript_exon	Exon 8 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNJL	ENST00000257536.13	TSL:2 MANE Select	c.930G>C	p.Arg310Arg	synonymous	Exon 6 of 6	ENSP00000257536.7	B4DZA8
	CCNJL	ENST00000393977.7	TSL:1	c.1074G>C	p.Arg358Arg	synonymous	Exon 7 of 7	ENSP00000377547.3	Q8IV13-1
	CCNJL	ENST00000870722.1		c.1008G>C	p.Arg336Arg	synonymous	Exon 6 of 6	ENSP00000540781.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	6.6
DANN	Benign	0.57
PhyloP100		0.93

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: chr5-159680619;