rs2861484

Positions:

• chr1-15486170-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015849.3(CELA2B):​c.639+124G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 1,256,708 control chromosomes in the GnomAD database, including 25,138 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 0.20 (3122 hom., cov: 32)
  • Exomes 𝑓: 0.20 (22016 hom.)
• Consequence: CELA2B NM_015849.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

CELA2B (HGNC:29995): (chymotrypsin like elastase 2B) Elastases form a subfamily of serine proteases that hydrolyze many proteins in addition to elastin. Humans have six elastase genes which encode the structurally similar proteins elastase 1, 2, 2A, 2B, 3A, and 3B. Like most of the human elastases, elastase 2B is secreted from the pancreas as a zymogen. In other species, elastase 2B has been shown to preferentially cleave proteins after leucine, methionine, and phenylalanine residues. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELA2B	NM_015849.3	c.639+124G>T		intron_variant		ENST00000375910.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELA2B	ENST00000375910.8	c.639+124G>T		intron_variant		1	NM_015849.3	P1
CELA2B	ENST00000488764.1	n.186+124G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29879 AN: 151980 Hom.: 3106 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.208

GnomAD4 exome AF: 0.195 AC: 215441 AN: 1104610 Hom.: 22016 AF XY: 0.196 AC XY: 107963 AN XY: 551264

Gnomad4 AFR exome AF: 0.202

Gnomad4 AMR exome AF: 0.117

Gnomad4 ASJ exome AF: 0.253

Gnomad4 EAS exome AF: 0.0671

Gnomad4 SAS exome AF: 0.204

Gnomad4 FIN exome AF: 0.216

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.197

GnomAD4 genome AF: 0.197 AC: 29920 AN: 152098 Hom.: 3122 Cov.: 32 AF XY: 0.195 AC XY: 14463 AN XY: 74350

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.206

Alfa AF: 0.202 Hom.: 1879

Bravo AF: 0.191

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.67

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: rs2861484; hg19: chr1-15812665;