chr14-57202815-A-G

Position:

• chr14-57202815-A-G

Variant summary

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

The NM_006544.4(EXOC5):​c.*5794T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,156 control chromosomes in the GnomAD database, including 4,561 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 0.21 (4561 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: EXOC5 NM_006544.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EXOC5	NM_006544.4	c.*5794T>C		3_prime_UTR_variant	18/18	ENST00000621441.5	NP_006535.1
EXOC5	XM_005267272.4	c.*5794T>C		3_prime_UTR_variant	18/18		XP_005267329.1
EXOC5	XM_047430882.1	c.*5794T>C		3_prime_UTR_variant	18/18		XP_047286838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EXOC5	ENST00000621441	c.*5794T>C		3_prime_UTR_variant	18/18	1	NM_006544.4	ENSP00000484855.1
EXOC5	ENST00000413566	c.*5794T>C		3_prime_UTR_variant	20/20

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31756 AN: 152036 Hom.: 4553 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.186

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.209 AC: 31796 AN: 152156 Hom.: 4561 Cov.: 32 AF XY: 0.202 AC XY: 15037 AN XY: 74400

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0959

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.185

Alfa AF: 0.162 Hom.: 1234

Bravo AF: 0.220

Asia WGS AF: 0.121 AC: 417 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.1
DANN	Benign	0.75

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: rs11851015; hg19: chr14-57669533;