chr6-35776992-C-G

Position:

• chr6-35776992-C-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLPSL2	NM_207409.4	c.84+290C>G		intron_variant		ENST00000403376.4
CLPSL2	NM_001286550.2	c.84+290C>G		intron_variant
CLPSL2	NR_104467.2	n.207+188C>G		intron_variant, non_coding_transcript_variant
CLPSL2	NR_104469.2	n.207+188C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLPSL2	ENST00000403376.4	c.84+290C>G		intron_variant		1	NM_207409.4	P1
CLPSL2	ENST00000360454.6	c.84+290C>G		intron_variant		1
CLPSL2	ENST00000467122.1	n.115+188C>G		intron_variant, non_coding_transcript_variant		3
CLPSL2	ENST00000481904.5	n.211+188C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.332

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.3
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs2296662; hg19: chr6-35744769;