7-133958268-CT-CTT

Variant names:

• chr7-133958268-C-CT
• rs5887652
• NM_021807.4:c.2206+20208dupT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_021807.4(EXOC4):​c.2206+20208dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (36800 hom., cov: 0)
• Consequence: EXOC4 NM_021807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXOC4	NM_021807.4	c.2206+20208dupT		intron_variant	Intron 14 of 17	ENST00000253861.5	NP_068579.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXOC4	ENST00000253861.5	c.2206+20199_2206+20200insT		intron_variant	Intron 14 of 17	1	NM_021807.4	ENSP00000253861.4
EXOC4	ENST00000850617.1	c.2206+20199_2206+20200insT		intron_variant	Intron 14 of 19			ENSP00000520904.1
EXOC4	ENST00000478265.1	n.452+20199_452+20200insT		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.697 AC: 104531 AN: 150022 Hom.: 36772 Cov.: 0

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.697 AC: 104604 AN: 150122 Hom.: 36800 Cov.: 0 AF XY: 0.701 AC XY: 51234 AN XY: 73134

African (AFR) AF: 0.717 AC: 29291 AN: 40856

American (AMR) AF: 0.762 AC: 11472 AN: 15060

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2257 AN: 3460

East Asian (EAS) AF: 0.908 AC: 4652 AN: 5126

South Asian (SAS) AF: 0.778 AC: 3686 AN: 4736

European-Finnish (FIN) AF: 0.680 AC: 6822 AN: 10034

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.654 AC: 44222 AN: 67572

Other (OTH) AF: 0.714 AC: 1488 AN: 2084

Alfa AF: 0.537 Hom.: 1082

Asia WGS AF: 0.822 AC: 2831 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.46
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

Other links and lift over

dbSNP: rs5887652; hg19: chr7-133643021;