3-157148445-A-G

Variant names:

• chr3-157148445-A-G
• rs1363086403
• NM_020307.4:c.1377T>C

Variant summary

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

The NM_020307.4(CCNL1):​c.1377T>C​(p.Ser459Ser) 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: 32)
• Consequence: CCNL1 NM_020307.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 0 publications found

Genes affected

CCNL1 (HGNC:20569): (cyclin L1) Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

LINC00881 (HGNC:48567): (long intergenic non-protein coding RNA 881)

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=-0.6).
• BP7: Synonymous conserved (PhyloP=-0.357 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020307.4. 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
	CCNL1	NM_020307.4	MANE Select	c.1377T>C	p.Ser459Ser	synonymous	Exon 11 of 11	NP_064703.1	Q9UK58-1
	CCNL1	NM_001308185.2		c.1232+842T>C		intron	N/A	NP_001295114.1	Q9UK58-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNL1	ENST00000295926.8	TSL:1 MANE Select	c.1377T>C	p.Ser459Ser	synonymous	Exon 11 of 11	ENSP00000295926.4	Q9UK58-1
	CCNL1	ENST00000464316.5	TSL:1	n.3193T>C		non_coding_transcript_exon	Exon 7 of 7
	CCNL1	ENST00000470121.5	TSL:1	n.*986T>C		non_coding_transcript_exon	Exon 13 of 13	ENSP00000417237.1	Q9UK58-4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.9
DANN	Benign	0.54
PhyloP100		-0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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

Other links and lift over

dbSNP: rs1363086403; hg19: chr3-156866234;