rs1856352

chr6-132459904-G-A

Variant summary

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

The NM_003569.3(STX7):c.*854C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 152,192 control chromosomes in the GnomAD database, including 279 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 0.057 (279 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: STX7 NM_003569.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STX7	NM_003569.3	c.*854C>T		3_prime_UTR_variant	10/10	ENST00000367941.7
STX7	NM_001326578.2	c.*854C>T		3_prime_UTR_variant	10/10
STX7	NM_001326579.2	c.*854C>T		3_prime_UTR_variant	10/10
STX7	NR_137169.2	n.1735C>T		non_coding_transcript_exon_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX7	ENST00000367941.7	c.*854C>T		3_prime_UTR_variant	10/10	1	NM_003569.3	P1

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8668 AN: 152074 Hom.: 279 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.0676

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0551

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0570 AC: 8668 AN: 152192 Hom.: 279 Cov.: 32 AF XY: 0.0573 AC XY: 4263 AN XY: 74386

Gnomad4 AFR AF: 0.0641

Gnomad4 AMR AF: 0.0550

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.0677

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0546

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.0532 Hom.: 33

Bravo AF: 0.0576

Asia WGS AF: 0.114 AC: 397 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.4
Dann	Benign	0.55

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: rs1856352; hg19: chr6-132781043;