Variant 2-79027823-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001008387.3(REG3G):c.350G>A(p.Gly117Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00416 in 1,614,008 control chromosomes in the GnomAD database, including 164 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 87 hom., cov: 32)

Exomes 𝑓: 0.0027 ( 77 hom. )

Consequence

REG3G
NM_001008387.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.134

Variant links:

Genes affected

REG3G (HGNC:29595): (regenerating family member 3 gamma) This gene encodes a member of the regenerating islet-derived genes (REG)3 protein family. These proteins are secreted, C-type lectins with a carbohydrate recognition domain and N-terminal signal peptide. The protein encoded by this gene is an antimicrobial lectin with activity against Gram-positive bacteria. Alternative splicing results in multiple transcript variants encoding multiple isoforms. [provided by RefSeq, Nov 2014]

REG3G links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0029760003).

BP6

Variant 2-79027823-G-A is Benign according to our data. Variant chr2-79027823-G-A is described in ClinVar as [Benign]. Clinvar id is 791859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
REG3G	NM_001008387.3 linkuse as main transcript	c.350G>A	p.Gly117Glu	missense_variant	5/6	ENST00000272324.10	NP_001008388.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REG3G	ENST00000272324.10 linkuse as main transcript	c.350G>A	p.Gly117Glu	missense_variant	5/6	1	NM_001008387.3	ENSP00000272324	P1	Q6UW15-1
REG3G	ENST00000393897.6 linkuse as main transcript	c.350G>A	p.Gly117Glu	missense_variant	5/6	1		ENSP00000377475	P1	Q6UW15-1
REG3G	ENST00000409471.1 linkuse as main transcript	c.212G>A	p.Gly71Glu	missense_variant	4/5	1		ENSP00000387105		Q6UW15-2

Frequencies

GnomAD3 genomes

AF:

0.0185

AC:

2821

AN:

152118

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0616

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00963

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00121

Gnomad OTH

AF:

0.0124

GnomAD3 exomes

AF:

0.00576

AC:

1445

AN:

250952

Hom.:

AF XY:

0.00440

AC XY:

597

AN XY:

135602

show subpopulations

Gnomad AFR exome

AF:

0.0667

Gnomad AMR exome

AF:

0.00468

Gnomad ASJ exome

AF:

0.000994

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000882

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00117

Gnomad OTH exome

AF:

0.00474

GnomAD4 exome

AF:

0.00265

AC:

3878

AN:

1461772

Hom.:

Cov.:

AF XY:

0.00238

AC XY:

1733

AN XY:

727190

show subpopulations

Gnomad4 AFR exome

AF:

0.0664

Gnomad4 AMR exome

AF:

0.00503

Gnomad4 ASJ exome

AF:

0.00130

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000754

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000844

Gnomad4 OTH exome

AF:

0.00535

GnomAD4 genome

AF:

0.0186

AC:

2838

AN:

152236

Hom.:

Cov.:

AF XY:

0.0178

AC XY:

1328

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.0619

Gnomad4 AMR

AF:

0.00955

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000830

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00121

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.00673

Hom.:

Bravo

AF:

0.0214

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.0608

AC:

268

ESP6500EA

AF:

0.00140

AC:

ExAC

AF:

0.00670

AC:

814

Asia WGS

AF:

0.00635

AC:

AN:

3478

EpiCase

AF:

0.00164

EpiControl

AF:

0.00184

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.78

CADD

Benign

8.4

DANN

Benign

0.96

DEOGEN2

Benign

0.0074

T;T;.

Eigen

Benign

-0.62

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.027

LIST_S2

Benign

0.67

.;T;T

MetaRNN

Benign

0.0030

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.41

N;N;.

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.36

PROVEAN

Uncertain

-3.4

D;D;D

REVEL

Benign

0.099

Sift

Benign

0.10

T;T;T

Sift4G

Benign

0.17

T;T;T

Polyphen

0.97

D;D;.

Vest4

0.30

MVP

0.39

MPC

0.031

ClinPred

0.038

GERP RS

-1.2

Varity_R

0.15

gMVP

0.25

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over