Variant chr17-76084241-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001013839.4(EXOC7):c.1818+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00924 in 1,611,834 control chromosomes in the GnomAD database, including 100 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0064 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0095 ( 94 hom. )

Consequence

EXOC7
NM_001013839.4 splice_region, intron

Scores

Splicing: ADA: 0.00008111

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.37

Variant links:

Genes affected

EXOC7 (HGNC:23214): (exocyst complex component 7) The protein encoded by this gene is a component of the exocyst complex. The exocyst complex plays a critical role in vesicular trafficking and the secretory pathway by targeting post-Golgi vesicles to the plasma membrane. The encoded protein is required for assembly of the exocyst complex and docking of the complex to the plasma membrane. The encoded protein may also play a role in pre-mRNA splicing through interactions with pre-mRNA-processing factor 19. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 4. [provided by RefSeq, Nov 2011]

EXOC7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 17-76084241-G-A is Benign according to our data. Variant chr17-76084241-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2648290.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EXOC7	NM_001013839.4 linkuse as main transcript	c.1818+7C>T		splice_region_variant, intron_variant		ENST00000589210.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EXOC7	ENST00000589210.6 linkuse as main transcript	c.1818+7C>T		splice_region_variant, intron_variant		1	NM_001013839.4		Q9UPT5-1

Frequencies

GnomAD3 genomes

AF:

0.00645

AC:

982

AN:

152136

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00412

Gnomad ASJ

AF:

0.0288

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00187

Gnomad FIN

AF:

0.00565

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00951

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00753

AC:

1888

AN:

250852

Hom.:

AF XY:

0.00762

AC XY:

1033

AN XY:

135650

show subpopulations

Gnomad AFR exome

AF:

0.00283

Gnomad AMR exome

AF:

0.00393

Gnomad ASJ exome

AF:

0.0334

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.00284

Gnomad FIN exome

AF:

0.00366

Gnomad NFE exome

AF:

0.0101

Gnomad OTH exome

AF:

0.00915

GnomAD4 exome

AF:

0.00953

AC:

13904

AN:

1459580

Hom.:

Cov.:

AF XY:

0.00946

AC XY:

6869

AN XY:

725752

show subpopulations

Gnomad4 AFR exome

AF:

0.00203

Gnomad4 AMR exome

AF:

0.00387

Gnomad4 ASJ exome

AF:

0.0327

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.00268

Gnomad4 FIN exome

AF:

0.00392

Gnomad4 NFE exome

AF:

0.0106

Gnomad4 OTH exome

AF:

0.00970

GnomAD4 genome

AF:

0.00645

AC:

982

AN:

152254

Hom.:

Cov.:

AF XY:

0.00591

AC XY:

440

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.00217

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.0288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.00565

Gnomad4 NFE

AF:

0.00951

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00827

Hom.:

Bravo

AF:

0.00668

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.0125

EpiControl

AF:

0.0119

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

EXOC7: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.056

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000081

dbscSNV1_RF

Benign

0.0040

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