dbSNP rs10165462: REG1A:n.116T>C (chr2-79120477-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000488524.1(REG1A):n.116T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 178,746 control chromosomes in the GnomAD database, including 11,335 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 0.31 ( 9428 hom., cov: 32)

Exomes 𝑓: 0.36 ( 1907 hom. )

Consequence

REG1A
ENST00000488524.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.541

Publications

8 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
REG1A	NM_002909.5 link	c.-84T>C		upstream_gene_variant		ENST00000233735.2	NP_002900.2	P05451A8K7G6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
REG1A	ENST00000488524.1 link	n.116T>C	non_coding_transcript_exon_variant	Exon 1 of 3	1
REG1A	ENST00000233735.2 link	c.-84T>C	upstream_gene_variant		1	NM_002909.5	ENSP00000233735.1	P05451
REG1A	ENST00000461579.1 link	n.-13T>C	upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47227

AN:

151930

Hom.:

9432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0756

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.457

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.565

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.293

GnomAD4 exome

AF:

0.358

AC:

9547

AN:

26698

Hom.:

1907

Cov.:

AF XY:

0.356

AC XY:

4818

AN XY:

13532

show subpopulations

African (AFR)

AF:

0.0615

AC:

AN:

1252

American (AMR)

AF:

0.316

AC:

251

AN:

794

Ashkenazi Jewish (ASJ)

AF:

0.282

AC:

346

AN:

1226

East Asian (EAS)

AF:

0.313

AC:

555

AN:

1774

South Asian (SAS)

AF:

0.281

AC:

AN:

210

European-Finnish (FIN)

AF:

0.491

AC:

683

AN:

1390

Middle Eastern (MID)

AF:

0.250

AC:

AN:

144

European-Non Finnish (NFE)

AF:

0.383

AC:

6912

AN:

18066

Other (OTH)

AF:

0.341

AC:

628

AN:

1842

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

298

597

895

1194

1492

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

192

240

<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:

0.311

AC:

47213

AN:

152048

Hom.:

9428

Cov.:

AF XY:

0.316

AC XY:

23499

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.0755

AC:

3132

AN:

41510

American (AMR)

AF:

0.299

AC:

4566

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.280

AC:

973

AN:

3472

East Asian (EAS)

AF:

0.457

AC:

2355

AN:

5156

South Asian (SAS)

AF:

0.336

AC:

1618

AN:

4812

European-Finnish (FIN)

AF:

0.565

AC:

5951

AN:

10542

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.406

AC:

27597

AN:

67958

Other (OTH)

AF:

0.293

AC:

620

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1491

2982

4473

5964

7455

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.352

Hom.:

2859

Bravo

AF:

0.282

Asia WGS

AF:

0.364

AC:

1269

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

0.54

PromoterAI

0.022

Neutral

(source)

Mutation Taster

=300/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over