12-116723068-G-C

Variant names:

• chr12-116723068-G-C
• NM_024738.4:c.267C>G
• SPRING1 p.Leu89Leu

Variant summary

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

The NM_024738.4(SPRING1):​c.267C>G​(p.Leu89Leu) variant causes a splice region, 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. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L89L) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SPRING1 NM_024738.4 splice_region, synonymous
• Scores: Splicing: ADA: 0.002416
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 0 publications found

Genes affected

SPRING1 (HGNC:26128): (SREBF pathway regulator in golgi 1) Involved in positive regulation of SREBP signaling pathway. Located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.74).
• BP7: Synonymous conserved (PhyloP=-1.92 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024738.4. 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
	SPRING1	NM_024738.4	MANE Select	c.267C>G	p.Leu89Leu	splice_region synonymous	Exon 2 of 5	NP_079014.1	Q9H741
	SPRING1	NM_001353623.2		c.179-2621C>G		intron	N/A	NP_001340552.1
	SPRING1	NM_001353624.2		c.112-3192C>G		intron	N/A	NP_001340553.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPRING1	ENST00000261318.5	TSL:1 MANE Select	c.267C>G	p.Leu89Leu	splice_region synonymous	Exon 2 of 5	ENSP00000261318.3	Q9H741
	SPRING1	ENST00000547630.1	TSL:1	n.112-2621C>G		intron	N/A	ENSP00000446478.1	F8VPB4
	SPRING1	ENST00000547606.1	TSL:3	c.46-5175C>G		intron	N/A	ENSP00000447722.1	H0YHS8

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	-0.74
CADD	Benign	0.70
DANN	Benign	0.61
PhyloP100		-1.9

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0024
dbscSNV1_RF	Benign	0.042
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: chr12-117160873;