dbSNP rs10483681: EXOC5:n.417A>G (chr14-57231956-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 ENST00000554011.5(EXOC5):n.417A>G 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 0.281 in 367,824 control chromosomes in the GnomAD database, including 15,874 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 ( 8074 hom., cov: 31)

Exomes 𝑓: 0.26 ( 7800 hom. )

Consequence

EXOC5
ENST00000554011.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.111

Publications

3 publications found

Variant links:

Genes affected

EXOC5 (HGNC:10696): (exocyst complex component 5) The protein encoded by this gene is a component of the exocyst complex, a multiple protein complex essential for targeting exocytic vesicles to specific docking sites on the plasma membrane. Though best characterized in yeast, the component proteins and functions of exocyst complex have been demonstrated to be highly conserved in higher eukaryotes. At least eight components of the exocyst complex, including this protein, are found to interact with the actin cytoskeletal remodeling and vesicle transport machinery. The complex is also essential for the biogenesis of epithelial cell surface polarity. [provided by RefSeq, Jul 2008]

EXOC5 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
EXOC5	NM_006544.4 link	c.939-241A>G	intron_variant	Intron 10 of 17	ENST00000621441.5	NP_006535.1	O00471
EXOC5	XM_005267272.4 link	c.1053-241A>G	intron_variant	Intron 10 of 17		XP_005267329.1
EXOC5	XM_047430882.1 link	c.774-241A>G	intron_variant	Intron 10 of 17		XP_047286838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXOC5	ENST00000621441.5 link	c.939-241A>G		intron_variant	Intron 10 of 17	1	NM_006544.4	ENSP00000484855.1		O00471

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47021

AN:

151866

Hom.:

8063

Cov.:

show subpopulations

Gnomad AFR

AF:

0.464

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.297

GnomAD4 exome

AF:

0.260

AC:

56214

AN:

215840

Hom.:

7800

Cov.:

AF XY:

0.260

AC XY:

29495

AN XY:

113404

show subpopulations

African (AFR)

AF:

0.469

AC:

2991

AN:

6378

American (AMR)

AF:

0.183

AC:

1345

AN:

7340

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

2316

AN:

7202

East Asian (EAS)

AF:

0.105

AC:

1466

AN:

13958

South Asian (SAS)

AF:

0.238

AC:

4997

AN:

21016

European-Finnish (FIN)

AF:

0.217

AC:

2297

AN:

10598

Middle Eastern (MID)

AF:

0.308

AC:

304

AN:

986

European-Non Finnish (NFE)

AF:

0.273

AC:

37026

AN:

135522

Other (OTH)

AF:

0.270

AC:

3472

AN:

12840

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1967

3935

5902

7870

9837

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

214

428

642

856

1070

<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:

0.310

AC:

47060

AN:

151984

Hom.:

8074

Cov.:

AF XY:

0.302

AC XY:

22428

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.464

AC:

19224

AN:

41406

American (AMR)

AF:

0.203

AC:

3107

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

1143

AN:

3472

East Asian (EAS)

AF:

0.134

AC:

691

AN:

5170

South Asian (SAS)

AF:

0.220

AC:

1063

AN:

4822

European-Finnish (FIN)

AF:

0.219

AC:

2316

AN:

10578

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.272

AC:

18481

AN:

67948

Other (OTH)

AF:

0.298

AC:

628

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1605

3210

4815

6420

8025

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

460

920

1380

1840

2300

<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:

0.283

Hom.:

4864

Bravo

AF:

0.314

Asia WGS

AF:

0.186

AC:

650

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.6

(source)

DANN

Benign

0.65

PhyloP100

-0.11

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