NM_207409.4:c.29G>C

Variant names:

• chr6-35776647-G-C
• rs1193062643
• NM_207409.4:c.29G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_207409.4(CLPSL2):​c.29G>C​(p.Gly10Ala) variant causes a missense 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CLPSL2 NM_207409.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.558
• Publications: 0 publications found

Genes affected

CLPSL2 (HGNC:21250): (colipase like 2) Predicted to enable enzyme activator activity. Predicted to be involved in response to food. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000307849 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0842714).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207409.4. 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
	CLPSL2	NM_207409.4	MANE Select	c.29G>C	p.Gly10Ala	missense	Exon 1 of 3	NP_997292.2	Q6UWE3-1
	CLPSL2	NM_001286550.2		c.29G>C	p.Gly10Ala	missense	Exon 1 of 4	NP_001273479.1	Q6UWE3-2
	CLPSL2	NR_104467.2		n.50G>C		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPSL2	ENST00000403376.4	TSL:1 MANE Select	c.29G>C	p.Gly10Ala	missense	Exon 1 of 3	ENSP00000385898.3	Q6UWE3-1
	CLPSL2	ENST00000360454.6	TSL:1	c.29G>C	p.Gly10Ala	missense	Exon 1 of 4	ENSP00000353639.2	Q6UWE3-2
	CLPSL2	ENST00000924056.1		c.29G>C	p.Gly10Ala	missense	Exon 1 of 2	ENSP00000594115.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000189

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.062
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	14
DANN	Benign	0.53
DEOGEN2	Benign	0.0053	T
Eigen	Benign	-0.87
Eigen_PC	Benign	-0.99
FATHMM_MKL	Benign	0.32	N
LIST_S2	Benign	0.47	T
M_CAP	Benign	0.0021	T
MetaRNN	Benign	0.084	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.0	L
PhyloP100		0.56
PrimateAI	Benign	0.48	T
PROVEAN	Uncertain	-3.0	D
REVEL	Benign	0.032
Sift	Benign	0.20	T
Sift4G	Pathogenic	0.0	D
Polyphen		0.70	P
Vest4		0.23
MutPred		0.32		Loss of helix (P = 0.0376)
MVP		0.014
MPC		0.047
ClinPred		0.28	T
GERP RS		0.87
PromoterAI		0.29	Neutral
Varity_R		0.052
gMVP		0.20
Mutation Taster		=100/0	polymorphism

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: rs1193062643; hg19: chr6-35744424;