dbSNP rs2070707: REG1A:c.64+145G>T (chr2-79121070-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002909.5(REG1A):c.64+145G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 621,096 control chromosomes in the GnomAD database, including 8,512 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 0.19 ( 3148 hom., cov: 31)

Exomes 𝑓: 0.14 ( 5364 hom. )

Consequence

REG1A
NM_002909.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.427

Publications

3 publications found

Variant links:

Genes affected

REG1A (HGNC:9951): (regenerating family member 1 alpha) This gene is a type I subclass member of the Reg gene family. The Reg gene family is a multigene family grouped into four subclasses, types I, II, III and IV, based on the primary structures of the encoded proteins. This gene encodes a protein that is secreted by the exocrine pancreas. It is associated with islet cell regeneration and diabetogenesis and may be involved in pancreatic lithogenesis. Reg family members REG1B, REGL, PAP and this gene are tandemly clustered on chromosome 2p12 and may have arisen from the same ancestral gene by gene duplication. [provided by RefSeq, Jul 2008]

REG1A links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002909.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REG1A	NM_002909.5	MANE Select	c.64+145G>T		intron	N/A	NP_002900.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
REG1A	ENST00000233735.2	TSL:1 MANE Select	c.64+145G>T	intron	N/A	ENSP00000233735.1	P05451
REG1A	ENST00000461579.1	TSL:1	n.436+145G>T	intron	N/A
REG1A	ENST00000488524.1	TSL:1	n.263+145G>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28013

AN:

150646

Hom.:

3139

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.0762

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.0636

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.190

GnomAD4 exome

AF:

0.139

AC:

65344

AN:

470388

Hom.:

5364

AF XY:

0.139

AC XY:

34170

AN XY:

246012

show subpopulations

African (AFR)

AF:

0.297

AC:

3866

AN:

13008

American (AMR)

AF:

0.193

AC:

3703

AN:

19226

Ashkenazi Jewish (ASJ)

AF:

0.207

AC:

2754

AN:

13328

East Asian (EAS)

AF:

0.179

AC:

5666

AN:

31674

South Asian (SAS)

AF:

0.171

AC:

6887

AN:

40388

European-Finnish (FIN)

AF:

0.0732

AC:

2652

AN:

36232

Middle Eastern (MID)

AF:

0.239

AC:

833

AN:

3482

European-Non Finnish (NFE)

AF:

0.121

AC:

34841

AN:

286762

Other (OTH)

AF:

0.158

AC:

4142

AN:

26288

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

2711

5422

8133

10844

13555

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

420

840

1260

1680

2100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.186

AC:

28048

AN:

150708

Hom.:

3148

Cov.:

AF XY:

0.185

AC XY:

13567

AN XY:

73396

show subpopulations

African (AFR)

AF:

0.307

AC:

12628

AN:

41096

American (AMR)

AF:

0.222

AC:

3355

AN:

15102

Ashkenazi Jewish (ASJ)

AF:

0.222

AC:

770

AN:

3470

East Asian (EAS)

AF:

0.155

AC:

790

AN:

5082

South Asian (SAS)

AF:

0.175

AC:

832

AN:

4752

European-Finnish (FIN)

AF:

0.0636

AC:

641

AN:

10086

Middle Eastern (MID)

AF:

0.252

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.125

AC:

8497

AN:

67854

Other (OTH)

AF:

0.190

AC:

394

AN:

2074

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1087

2175

3262

4350

5437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

288

576

864

1152

1440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.167

Hom.:

422

Bravo

AF:

0.200

Asia WGS

AF:

0.174

AC:

606

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

4.4

(source)

DANN

Benign

0.35

PhyloP100

0.43

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over