dbSNP rs328406: GARRE1:c.2687+51C>T (chr19-34348093-C-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_014686.5(GARRE1):c.2687+51C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,363,960 control chromosomes in the GnomAD database, including 41,916 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 ( 4427 hom., cov: 32)

Exomes 𝑓: 0.24 ( 37489 hom. )

Consequence

GARRE1
NM_014686.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.746

Publications

8 publications found

Variant links:

Genes affected

GARRE1 (HGNC:29016): (granule associated Rac and RHOG effector 1) Enables CCR4-NOT complex binding activity and small GTPase binding activity. Involved in Rac protein signal transduction. Located in P-body. [provided by Alliance of Genome Resources, Apr 2022]

GARRE1 links:

ENSG00000267219 (HGNC:):

ENSG00000267219 links:

Genome browser will be placed here

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GARRE1	NM_014686.5 link	c.2687+51C>T		intron_variant	Intron 11 of 13	ENST00000299505.8	NP_055501.2	O15063

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GARRE1	ENST00000299505.8 link	c.2687+51C>T		intron_variant	Intron 11 of 13	1	NM_014686.5	ENSP00000299505.4		O15063

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34186

AN:

152034

Hom.:

4424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.177

Gnomad AMI

AF:

0.217

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.617

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.249

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.225

GnomAD2 exomes

AF:

0.254

AC:

29028

AN:

114466

AF XY:

0.251

show subpopulations

Gnomad AFR exome

AF:

0.179

Gnomad AMR exome

AF:

0.239

Gnomad ASJ exome

AF:

0.218

Gnomad EAS exome

AF:

0.624

Gnomad FIN exome

AF:

0.258

Gnomad NFE exome

AF:

0.226

Gnomad OTH exome

AF:

0.235

GnomAD4 exome

AF:

0.238

AC:

288080

AN:

1211806

Hom.:

37489

Cov.:

AF XY:

0.237

AC XY:

139199

AN XY:

587356

show subpopulations

African (AFR)

AF:

0.171

AC:

4329

AN:

25264

American (AMR)

AF:

0.222

AC:

3989

AN:

18004

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

3508

AN:

16732

East Asian (EAS)

AF:

0.663

AC:

20484

AN:

30878

South Asian (SAS)

AF:

0.205

AC:

9636

AN:

47108

European-Finnish (FIN)

AF:

0.255

AC:

11313

AN:

44378

Middle Eastern (MID)

AF:

0.171

AC:

550

AN:

3216

European-Non Finnish (NFE)

AF:

0.227

AC:

222166

AN:

977638

Other (OTH)

AF:

0.249

AC:

12105

AN:

48588

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

10580

21160

31741

42321

52901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8486

16972

25458

33944

42430

<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:

0.225

AC:

34198

AN:

152154

Hom.:

4427

Cov.:

AF XY:

0.227

AC XY:

16877

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.177

AC:

7332

AN:

41490

American (AMR)

AF:

0.194

AC:

2971

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

754

AN:

3470

East Asian (EAS)

AF:

0.618

AC:

3194

AN:

5170

South Asian (SAS)

AF:

0.214

AC:

1035

AN:

4828

European-Finnish (FIN)

AF:

0.249

AC:

2644

AN:

10598

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.229

AC:

15543

AN:

67996

Other (OTH)

AF:

0.224

AC:

471

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1349

2698

4046

5395

6744

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:

0.232

Hom.:

671

Bravo

AF:

0.221

Asia WGS

AF:

0.380

AC:

1321

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.68

(source)

DANN

Benign

0.49

PhyloP100

-0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over