rs6971064

Variant names:

• chr7-134055511-C-A
• rs6971064
• NM_021807.4:c.2688-8780C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-134055511-C-A
• chr7-134055511-C-T

Variant summary

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

The ENST00000253861.5(EXOC4):​c.2688-8780C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,194 control chromosomes in the GnomAD database, including 2,715 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 0.18 (2715 hom., cov: 32)
• Consequence: EXOC4 ENST00000253861.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000253861.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXOC4	NM_021807.4	MANE Select	c.2688-8780C>A		intron	N/A	NP_068579.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXOC4	ENST00000253861.5	TSL:1 MANE Select	c.2688-8780C>A		intron	N/A	ENSP00000253861.4
	EXOC4	ENST00000850617.1		c.2688-8780C>A		intron	N/A	ENSP00000520904.1
	EXOC4	ENST00000459626.1	TSL:3	n.425-8780C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26623 AN: 152076 Hom.: 2708 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.175 AC: 26669 AN: 152194 Hom.: 2715 Cov.: 32 AF XY: 0.170 AC XY: 12662 AN XY: 74424

African (AFR) AF: 0.271 AC: 11233 AN: 41504

American (AMR) AF: 0.173 AC: 2650 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3470

East Asian (EAS) AF: 0.172 AC: 886 AN: 5166

South Asian (SAS) AF: 0.129 AC: 625 AN: 4832

European-Finnish (FIN) AF: 0.0870 AC: 923 AN: 10606

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9224 AN: 68002

Other (OTH) AF: 0.205 AC: 433 AN: 2112

Alfa AF: 0.125 Hom.: 681

Bravo AF: 0.189

Asia WGS AF: 0.163 AC: 564 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.29
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: rs6971064; hg19: chr7-133740264;