rs11169806

chr12-51337207-C-Achr12-51337207-C-Gchr12-51337207-C-T

Variant summary

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

The NM_001971.6(CELA1):c.609+2653G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,962 control chromosomes in the GnomAD database, including 13,356 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 0.41 (13356 hom., cov: 31)
• Consequence: CELA1 NM_001971.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93

Genes affected

CELA1 (HGNC:3308): (chymotrypsin like elastase 1) 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. Unlike other elastases, pancreatic elastase 1 is not expressed in the pancreas. To date, elastase 1 expression has only been detected in skin keratinocytes. Clinical literature that describes human elastase 1 activity in the pancreas or fecal material is actually referring to chymotrypsin-like elastase family, member 3B. [provided by RefSeq, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELA1	NM_001971.6	c.609+2653G>T		intron_variant		ENST00000293636.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELA1	ENST00000293636.2	c.609+2653G>T		intron_variant		1	NM_001971.6	P1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62694 AN: 151846 Hom.: 13341 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.413 AC: 62752 AN: 151962 Hom.: 13356 Cov.: 31 AF XY: 0.415 AC XY: 30822 AN XY: 74236

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.436

Alfa AF: 0.233 Hom.: 487

Bravo AF: 0.427

Asia WGS AF: 0.448 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.24
Dann	Benign	0.70

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: rs11169806; hg19: chr12-51730991;