6-132480736-A-G

Variant names:

• chr6-132480736-A-G
• rs1002799
• NM_003569.3:c.86-5074T>C

Variant summary

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

The NM_003569.3(STX7):​c.86-5074T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,158 control chromosomes in the GnomAD database, including 5,350 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 0.25 (5350 hom., cov: 32)
• Consequence: STX7 NM_003569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 6 publications found

Genes affected

STX7 (HGNC:11442): (syntaxin 7) The protein encoded by this gene is a syntaxin family membrane receptor involved in vesicle transport. The encoded protein binds alpha-SNAP, an important regulator of transport vesicle fusion. Along with syntaxin 13, this protein plays a role in the ordered fusion of endosomes and lysosomes with the phagosome. [provided by RefSeq, May 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003569.3. 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
	STX7	NM_003569.3	MANE Select	c.86-5074T>C		intron	N/A	NP_003560.2
	STX7	NM_001326578.2		c.86-5074T>C		intron	N/A	NP_001313507.1
	STX7	NM_001326579.2		c.86-5074T>C		intron	N/A	NP_001313508.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STX7	ENST00000367941.7	TSL:1 MANE Select	c.86-5074T>C		intron	N/A	ENSP00000356918.1
	STX7	ENST00000862289.1		c.86-5074T>C		intron	N/A	ENSP00000532348.1
	STX7	ENST00000862290.1		c.86-5074T>C		intron	N/A	ENSP00000532349.1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37882 AN: 152040 Hom.: 5350 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.249 AC: 37895 AN: 152158 Hom.: 5350 Cov.: 32 AF XY: 0.254 AC XY: 18901 AN XY: 74390

African (AFR) AF: 0.286 AC: 11872 AN: 41514

American (AMR) AF: 0.265 AC: 4062 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 755 AN: 3472

East Asian (EAS) AF: 0.648 AC: 3348 AN: 5166

South Asian (SAS) AF: 0.353 AC: 1701 AN: 4812

European-Finnish (FIN) AF: 0.179 AC: 1894 AN: 10602

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.198 AC: 13490 AN: 67978

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.214 Hom.: 5073

Bravo AF: 0.254

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.88
PhyloP100		0.022
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs1002799; hg19: chr6-132801875;