rs2178689

Positions:

• chr7-133268943-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021807.4(EXOC4):​c.87-6039A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,200 control chromosomes in the GnomAD database, including 58,104 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 0.87 (58104 hom., cov: 32)
• Consequence: EXOC4 NM_021807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

Genes affected

EXOC4 (HGNC:30389): (exocyst complex component 4) 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. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EXOC4	NM_021807.4	c.87-6039A>T		intron_variant		ENST00000253861.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EXOC4	ENST00000253861.5	c.87-6039A>T		intron_variant		1	NM_021807.4	P1

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132276 AN: 152082 Hom.: 58040 Cov.: 32

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.870

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.870 AC: 132400 AN: 152200 Hom.: 58104 Cov.: 32 AF XY: 0.871 AC XY: 64853 AN XY: 74416

Gnomad4 AFR AF: 0.967

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.871

Alfa AF: 0.846 Hom.: 6825

Bravo AF: 0.877

Asia WGS AF: 0.958 AC: 3327 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	14
DANN	Benign	0.87

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

Other links and lift over

dbSNP: rs2178689; hg19: chr7-132953698;