6-132478405-C-T

Position:

• chr6-132478405-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003569.3(STX7):​c.86-2743G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,012 control chromosomes in the GnomAD database, including 4,463 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 0.23 (4463 hom., cov: 32)
• Consequence: STX7 NM_003569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STX7	NM_003569.3	c.86-2743G>A		intron_variant		ENST00000367941.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX7	ENST00000367941.7	c.86-2743G>A		intron_variant		1	NM_003569.3	P1
STX7	ENST00000367937.4	c.86-2743G>A		intron_variant		5
STX7	ENST00000448348.3	n.148-2743G>A		intron_variant, non_coding_transcript_variant		4
STX7	ENST00000475879.1	n.203-2743G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35107 AN: 151894 Hom.: 4458 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.231 AC: 35137 AN: 152012 Hom.: 4463 Cov.: 32 AF XY: 0.238 AC XY: 17703 AN XY: 74322

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.259

Alfa AF: 0.225 Hom.: 6527

Bravo AF: 0.230

Asia WGS AF: 0.433 AC: 1503 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs9493329; hg19: chr6-132799544;