7-133781255-C-T

Variant names:

• chr7-133781255-C-T
• rs1073158
• NM_021807.4:c.1515-36070C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021807.4(EXOC4):​c.1515-36070C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,240 control chromosomes in the GnomAD database, including 56,805 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 0.86 (56805 hom., cov: 34)
• Consequence: EXOC4 NM_021807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXOC4	NM_021807.4	c.1515-36070C>T		intron_variant	Intron 10 of 17	ENST00000253861.5	NP_068579.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXOC4	ENST00000253861.5	c.1515-36070C>T		intron_variant	Intron 10 of 17	1	NM_021807.4	ENSP00000253861.4

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131220 AN: 152122 Hom.: 56753 Cov.: 34

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.863 AC: 131332 AN: 152240 Hom.: 56805 Cov.: 34 AF XY: 0.864 AC XY: 64311 AN XY: 74426

African (AFR) AF: 0.813 AC: 33763 AN: 41538

American (AMR) AF: 0.910 AC: 13919 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3146 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5138 AN: 5170

South Asian (SAS) AF: 0.914 AC: 4413 AN: 4828

European-Finnish (FIN) AF: 0.849 AC: 8996 AN: 10602

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59045 AN: 68012

Other (OTH) AF: 0.890 AC: 1877 AN: 2110

Alfa AF: 0.871 Hom.: 29287

Bravo AF: 0.867

Asia WGS AF: 0.940 AC: 3268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.75
DANN	Benign	0.47
PhyloP100		-0.35
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: rs1073158; hg19: chr7-133466008;