rs1856352

Variant names:

• chr6-132459904-G-A
• rs1856352
• NM_003569.3:c.*854C>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.*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
• 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=-0.87).
• 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 rank	MANE	Protein	UniProt
STX7	NM_003569.3	c.*854C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000367941.7	NP_003560.2
STX7	NR_137169.2	n.1735C>T		non_coding_transcript_exon_variant	Exon 9 of 9
STX7	NM_001326578.2	c.*854C>T		3_prime_UTR_variant	Exon 10 of 10		NP_001313507.1
STX7	NM_001326579.2	c.*854C>T		3_prime_UTR_variant	Exon 10 of 10		NP_001313508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STX7	ENST00000367941.7	c.*854C>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_003569.3	ENSP00000356918.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0641 AC: 2662 AN: 41524

American (AMR) AF: 0.0550 AC: 841 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0701 AC: 243 AN: 3468

East Asian (EAS) AF: 0.0677 AC: 351 AN: 5184

South Asian (SAS) AF: 0.111 AC: 538 AN: 4830

European-Finnish (FIN) AF: 0.0546 AC: 578 AN: 10582

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0487 AC: 3315 AN: 68006

Other (OTH) AF: 0.0545 AC: 115 AN: 2110

Alfa AF: 0.0559 Hom.: 147

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
PhyloP100		-0.035
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: rs1856352; hg19: chr6-132781043;