chr6-132492898-G-A

Variant names:

• chr6-132492898-G-A
• rs2788942
• NM_003569.3:c.85+10548C>T

Variant summary

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

The NM_003569.3(STX7):​c.85+10548C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,056 control chromosomes in the GnomAD database, including 30,172 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 0.63 (30172 hom., cov: 32)
• Consequence: STX7 NM_003569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STX7	NM_003569.3	c.85+10548C>T		intron_variant	Intron 2 of 9	ENST00000367941.7	NP_003560.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STX7	ENST00000367941.7	c.85+10548C>T		intron_variant	Intron 2 of 9	1	NM_003569.3	ENSP00000356918.1
STX7	ENST00000367937.4	c.85+10548C>T		intron_variant	Intron 2 of 9	5		ENSP00000356914.4
STX7	ENST00000448348.3	n.147+10548C>T		intron_variant	Intron 2 of 6	4
STX7	ENST00000475879.1	n.202+10548C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95312 AN: 151938 Hom.: 30148 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.627 AC: 95375 AN: 152056 Hom.: 30172 Cov.: 32 AF XY: 0.623 AC XY: 46309 AN XY: 74316

African (AFR) AF: 0.706 AC: 29266 AN: 41480

American (AMR) AF: 0.590 AC: 9020 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2474 AN: 3470

East Asian (EAS) AF: 0.646 AC: 3336 AN: 5168

South Asian (SAS) AF: 0.585 AC: 2819 AN: 4822

European-Finnish (FIN) AF: 0.519 AC: 5479 AN: 10556

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40814 AN: 67964

Other (OTH) AF: 0.651 AC: 1374 AN: 2112

Alfa AF: 0.615 Hom.: 43600

Bravo AF: 0.637

Asia WGS AF: 0.562 AC: 1953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.73
DANN	Benign	0.37
PhyloP100		-0.27
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: rs2788942; hg19: chr6-132814037;