rs3823572

Variant names:

• chr7-133995848-G-A
• rs3823572
• NM_021807.4:c.2207-1644G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-133995848-G-A
• chr7-133995848-G-C

Variant summary

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

The NM_021807.4(EXOC4):​c.2207-1644G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,912 control chromosomes in the GnomAD database, including 21,148 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 0.51 (21148 hom., cov: 31)
• Consequence: EXOC4 NM_021807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXOC4	NM_021807.4	c.2207-1644G>A		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.2207-1644G>A		intron_variant	Intron 14 of 17	1	NM_021807.4	ENSP00000253861.4
EXOC4	ENST00000850617.1	c.2207-1644G>A		intron_variant	Intron 14 of 19			ENSP00000520904.1
EXOC4	ENST00000478265.1	n.453-1644G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77808 AN: 151794 Hom.: 21137 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.513 AC: 77865 AN: 151912 Hom.: 21148 Cov.: 31 AF XY: 0.512 AC XY: 38008 AN XY: 74264

African (AFR) AF: 0.678 AC: 28088 AN: 41456

American (AMR) AF: 0.386 AC: 5881 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1189 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2469 AN: 5162

South Asian (SAS) AF: 0.597 AC: 2866 AN: 4804

European-Finnish (FIN) AF: 0.467 AC: 4933 AN: 10556

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30857 AN: 67898

Other (OTH) AF: 0.509 AC: 1073 AN: 2110

Alfa AF: 0.465 Hom.: 27905

Bravo AF: 0.510

Asia WGS AF: 0.539 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.23
PhyloP100		-0.041
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: rs3823572; hg19: chr7-133680601;