6-499672-C-A

Variant names:

• chr6-499672-C-A
• rs80011872
• NM_018303.6:c.2409G>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Moderate BP6_Moderate BP7 BA1

The NM_018303.6(EXOC2):​c.2409G>T​(p.Leu803Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00295 in 1,613,582 control chromosomes in the GnomAD database, including 141 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.016 (82 hom., cov: 32)
  • Exomes 𝑓: 0.0016 (59 hom.)
• Consequence: EXOC2 NM_018303.6 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.11

Genes affected

EXOC2 (HGNC:24968): (exocyst complex component 2) The protein encoded by this gene is a component of the exocyst complex, a multi-protein complex essential for the polarized targeting of exocytic vesicles to specific docking sites on the plasma membrane. Though best characterized in yeast, the component proteins and the functions of the 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. This interaction has been shown to mediate filopodia formation in fibroblasts. This protein has been shown to interact with the Ral subfamily of GTPases and thereby mediate exocytosis by tethering vesicles to the plasma membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BP6: Variant 6-499672-C-A is Benign according to our data. Variant chr6-499672-C-A is described in ClinVar as [Benign]. Clinvar id is 789742.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=2.11 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXOC2	NM_018303.6	c.2409G>T	p.Leu803Leu	synonymous_variant	Exon 24 of 28	ENST00000230449.9	NP_060773.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXOC2	ENST00000230449.9	c.2409G>T	p.Leu803Leu	synonymous_variant	Exon 24 of 28	1	NM_018303.6	ENSP00000230449.4

Frequencies

GnomAD3 genomes AF: 0.0162 AC: 2465 AN: 151950 Hom.: 81 Cov.: 32

Gnomad AFR AF: 0.0547

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00976

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000426

Gnomad OTH AF: 0.0120

GnomAD2 exomes AF: 0.00448 AC: 1126 AN: 251274 AF XY: 0.00317

Gnomad AFR exome AF: 0.0567

Gnomad AMR exome AF: 0.00431

Gnomad ASJ exome AF: 0.0000993

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000334

Gnomad OTH exome AF: 0.00293

GnomAD4 exome AF: 0.00157 AC: 2293 AN: 1461514 Hom.: 59 Cov.: 30 AF XY: 0.00127 AC XY: 926 AN XY: 727062

Gnomad4 AFR exome AF: 0.0499 AC: 1668 AN: 33428

Gnomad4 AMR exome AF: 0.00470 AC: 210 AN: 44716

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 26128

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39672

Gnomad4 SAS exome AF: 0.0000696 AC: 6 AN: 86238

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 53412

Gnomad4 NFE exome AF: 0.000148 AC: 165 AN: 1111782

Gnomad4 Remaining exome AF: 0.00391 AC: 236 AN: 60372

GnomAD4 genome AF: 0.0162 AC: 2470 AN: 152068 Hom.: 82 Cov.: 32 AF XY: 0.0158 AC XY: 1173 AN XY: 74346

Gnomad4 AFR AF: 0.0547 AC: 0.0546867 AN: 0.0546867

Gnomad4 AMR AF: 0.00975 AC: 0.00974876 AN: 0.00974876

Gnomad4 ASJ AF: 0.00 AC: 0 AN: 0

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000208 AC: 0.000207555 AN: 0.000207555

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.000426 AC: 0.000426496 AN: 0.000426496

Gnomad4 OTH AF: 0.0118 AC: 0.0118483 AN: 0.0118483

Alfa AF: 0.00725 Hom.: 30

Bravo AF: 0.0186

Asia WGS AF: 0.00202 AC: 7 AN: 3478

EpiCase AF: 0.000436

EpiControl AF: 0.000534

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 13, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	11
DANN	Benign	0.78
Mutation Taster		=100/0	polymorphism (auto)

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: rs80011872; hg19: chr6-499672;