Variant 17-76081416-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001013839.4(EXOC7):c.*2232C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 1,613,742 control chromosomes in the GnomAD database, including 277,561 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 0.44 ( 18228 hom., cov: 33)

Exomes 𝑓: 0.59 ( 259333 hom. )

Consequence

EXOC7
NM_001013839.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.00

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:

ZACN (HGNC:29504): (zinc activated ion channel) LGICZ1 is a zinc-activated ligand-gated ion channel that defines a new subgroup of the cysteine-loop superfamily of ligand-gated ion channels (Davies et al., 2003 [PubMed 12381728]).[supplied by OMIM, Mar 2008]

ZACN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EXOC7	NM_001013839.4 linkuse as main transcript	c.*2232C>G		3_prime_UTR_variant	19/19	ENST00000589210.6
ZACN	NM_180990.4 linkuse as main transcript	c.669+14G>C		intron_variant		ENST00000334586.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EXOC7	ENST00000589210.6 linkuse as main transcript	c.*2232C>G		3_prime_UTR_variant	19/19	1	NM_001013839.4		Q9UPT5-1
ZACN	ENST00000334586.10 linkuse as main transcript	c.669+14G>C		intron_variant		1	NM_180990.4	P1	Q401N2-1

Frequencies

GnomAD3 genomes

AF:

0.443

AC:

67341

AN:

152080

Hom.:

18225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.442

Gnomad AMR

AF:

0.392

Gnomad ASJ

AF:

0.548

Gnomad EAS

AF:

0.486

Gnomad SAS

AF:

0.687

Gnomad FIN

AF:

0.593

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.599

Gnomad OTH

AF:

0.449

GnomAD3 exomes

AF:

0.538

AC:

134915

AN:

250844

Hom.:

39057

AF XY:

0.557

AC XY:

75517

AN XY:

135642

show subpopulations

Gnomad AFR exome

AF:

0.109

Gnomad AMR exome

AF:

0.399

Gnomad ASJ exome

AF:

0.562

Gnomad EAS exome

AF:

0.468

Gnomad SAS exome

AF:

0.676

Gnomad FIN exome

AF:

0.596

Gnomad NFE exome

AF:

0.602

Gnomad OTH exome

AF:

0.550

GnomAD4 exome

AF:

0.588

AC:

859713

AN:

1461544

Hom.:

259333

Cov.:

AF XY:

0.593

AC XY:

431169

AN XY:

727078

show subpopulations

Gnomad4 AFR exome

AF:

0.0993

Gnomad4 AMR exome

AF:

0.400

Gnomad4 ASJ exome

AF:

0.559

Gnomad4 EAS exome

AF:

0.469

Gnomad4 SAS exome

AF:

0.677

Gnomad4 FIN exome

AF:

0.600

Gnomad4 NFE exome

AF:

0.610

Gnomad4 OTH exome

AF:

0.561

GnomAD4 genome

AF:

0.442

AC:

67343

AN:

152198

Hom.:

18228

Cov.:

AF XY:

0.444

AC XY:

33027

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.124

Gnomad4 AMR

AF:

0.391

Gnomad4 ASJ

AF:

0.548

Gnomad4 EAS

AF:

0.487

Gnomad4 SAS

AF:

0.689

Gnomad4 FIN

AF:

0.593

Gnomad4 NFE

AF:

0.599

Gnomad4 OTH

AF:

0.448

Alfa

AF:

0.454

Hom.:

2582

Bravo

AF:

0.408

Asia WGS

AF:

0.534

AC:

1853

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

7.1

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over