rs7457999

Positions:

• chr7-134063482-T-C
• chr7-134063482-T-G

Variant summary

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

The NM_021807.4(EXOC4):​c.2688-809T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,082 control chromosomes in the GnomAD database, including 8,076 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 0.31 (8076 hom., cov: 32)
• Consequence: EXOC4 NM_021807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EXOC4	NM_021807.4	c.2688-809T>C		intron_variant		ENST00000253861.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EXOC4	ENST00000253861.5	c.2688-809T>C		intron_variant		1	NM_021807.4	P1
EXOC4	ENST00000459626.1	n.425-809T>C		intron_variant, non_coding_transcript_variant		3
EXOC4	ENST00000466000.1	n.236-809T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47601 AN: 151966 Hom.: 8052 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.313 AC: 47674 AN: 152082 Hom.: 8076 Cov.: 32 AF XY: 0.315 AC XY: 23400 AN XY: 74382

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.302

Alfa AF: 0.247 Hom.: 4948

Bravo AF: 0.324

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.61

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: rs7457999; hg19: chr7-133748235;