6-35776992-C-G

Variant names:

• chr6-35776992-C-G
• rs2296662
• NM_207409.4:c.84+290C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207409.4(CLPSL2):​c.84+290C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,888 control chromosomes in the GnomAD database, including 9,583 homozygotes. 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: 𝑓 0.35 (9583 hom., cov: 31)
• Consequence: CLPSL2 NM_207409.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPSL2	NM_207409.4	MANE Select	c.84+290C>G		intron	N/A	NP_997292.2
	CLPSL2	NM_001286550.2		c.84+290C>G		intron	N/A	NP_001273479.1
	CLPSL2	NR_104467.2		n.207+188C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPSL2	ENST00000403376.4	TSL:1 MANE Select	c.84+290C>G		intron	N/A	ENSP00000385898.3
	CLPSL2	ENST00000360454.6	TSL:1	c.84+290C>G		intron	N/A	ENSP00000353639.2
	CLPSL2	ENST00000467122.1	TSL:3	n.115+188C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53731 AN: 151772 Hom.: 9560 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.326

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.354 AC: 53799 AN: 151888 Hom.: 9583 Cov.: 31 AF XY: 0.357 AC XY: 26495 AN XY: 74212

African (AFR) AF: 0.336 AC: 13945 AN: 41448

American (AMR) AF: 0.401 AC: 6120 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2290 AN: 5130

South Asian (SAS) AF: 0.318 AC: 1535 AN: 4820

European-Finnish (FIN) AF: 0.398 AC: 4192 AN: 10530

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23835 AN: 67926

Other (OTH) AF: 0.332 AC: 699 AN: 2108

Alfa AF: 0.216 Hom.: 481

Bravo AF: 0.359

Asia WGS AF: 0.419 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.3
DANN	Benign	0.77
PhyloP100		-0.52
PromoterAI		0.077	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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: rs2296662; hg19: chr6-35744769;