Genetic Variant GARIN1B:p.Leu147Leu (chr7-128718837-C-A) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001282788.3(GARIN1B):c.441C>A(p.Leu147Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,613,088 control chromosomes in the GnomAD database, including 42,528 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 0.22 ( 3655 hom., cov: 31)

Exomes 𝑓: 0.23 ( 38873 hom. )

Consequence

GARIN1B
NM_001282788.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.496

Publications

15 publications found

Variant links:

Genes affected

GARIN1B (HGNC:30704): (golgi associated RAB2 interactor 1B)

GARIN1B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP7

Synonymous conserved (PhyloP=0.496 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GARIN1B	NM_001282788.3 link	c.441C>A	p.Leu147Leu	synonymous_variant	Exon 3 of 7	ENST00000621392.5	NP_001269717.1	Q96KD3-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GARIN1B	ENST00000621392.5 link	c.441C>A	p.Leu147Leu	synonymous_variant	Exon 3 of 7	5	NM_001282788.3	ENSP00000477573.2		Q96KD3-2

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33192

AN:

151986

Hom.:

3649

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.213

GnomAD2 exomes

AF:

0.211

AC:

52932

AN:

250356

AF XY:

0.217

show subpopulations

Gnomad AFR exome

AF:

0.214

Gnomad AMR exome

AF:

0.116

Gnomad ASJ exome

AF:

0.190

Gnomad EAS exome

AF:

0.114

Gnomad FIN exome

AF:

0.242

Gnomad NFE exome

AF:

0.233

Gnomad OTH exome

AF:

0.200

GnomAD4 exome

AF:

0.227

AC:

332064

AN:

1460984

Hom.:

38873

Cov.:

AF XY:

0.229

AC XY:

166605

AN XY:

726650

show subpopulations

African (AFR)

AF:

0.219

AC:

7335

AN:

33470

American (AMR)

AF:

0.120

AC:

5376

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.189

AC:

4937

AN:

26126

East Asian (EAS)

AF:

0.122

AC:

4821

AN:

39674

South Asian (SAS)

AF:

0.286

AC:

24655

AN:

86246

European-Finnish (FIN)

AF:

0.241

AC:

12855

AN:

53378

Middle Eastern (MID)

AF:

0.207

AC:

1193

AN:

5768

European-Non Finnish (NFE)

AF:

0.232

AC:

257499

AN:

1111232

Other (OTH)

AF:

0.222

AC:

13393

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

13079

26159

39238

52318

65397

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8778

17556

26334

35112

43890

<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:

0.218

AC:

33215

AN:

152104

Hom.:

3655

Cov.:

AF XY:

0.218

AC XY:

16211

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.216

AC:

8979

AN:

41494

American (AMR)

AF:

0.165

AC:

2518

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.191

AC:

662

AN:

3470

East Asian (EAS)

AF:

0.114

AC:

588

AN:

5176

South Asian (SAS)

AF:

0.273

AC:

1316

AN:

4828

European-Finnish (FIN)

AF:

0.248

AC:

2621

AN:

10562

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.234

AC:

15880

AN:

67972

Other (OTH)

AF:

0.217

AC:

458

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1348

2696

4044

5392

6740

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

370

740

1110

1480

1850

<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:

0.224

Hom.:

16315

Bravo

AF:

0.205

Asia WGS

AF:

0.202

AC:

705

AN:

3478

EpiCase

AF:

0.226

EpiControl

AF:

0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.27

CADD

Benign

8.0

(source)

DANN

Benign

0.74

PhyloP100

0.50

PromoterAI

0.011

Neutral

(source)

Mutation Taster

=99/1

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