NM_001971.6:c.609+2653G>T

Variant names:

• chr12-51337207-C-A
• rs11169806
• NM_001971.6:c.609+2653G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001971.6. 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
	CELA1	NM_001971.6	MANE Select	c.609+2653G>T		intron	N/A	NP_001962.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELA1	ENST00000293636.2	TSL:1 MANE Select	c.609+2653G>T		intron	N/A	ENSP00000293636.1

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

African (AFR) AF: 0.367 AC: 15201 AN: 41444

American (AMR) AF: 0.520 AC: 7923 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1325 AN: 3470

East Asian (EAS) AF: 0.579 AC: 2985 AN: 5156

South Asian (SAS) AF: 0.331 AC: 1594 AN: 4816

European-Finnish (FIN) AF: 0.366 AC: 3861 AN: 10546

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28419 AN: 67976

Other (OTH) AF: 0.436 AC: 921 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.70
PhyloP100		-2.9
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: rs11169806; hg19: chr12-51730991;