chr6-132503840-G-C

Position:

• chr6-132503840-G-C

Variant summary

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

The NM_003569.3(STX7):​c.-58-252C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,674 control chromosomes in the GnomAD database, including 9,356 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 0.34 (9356 hom., cov: 32)
• Consequence: STX7 NM_003569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

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 (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STX7	NM_003569.3	c.-58-252C>G		intron_variant		ENST00000367941.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX7	ENST00000367941.7	c.-58-252C>G		intron_variant		1	NM_003569.3	P1
STX7	ENST00000367937.4	c.-58-252C>G		intron_variant		5
STX7	ENST00000448348.3	n.79-326C>G		intron_variant, non_coding_transcript_variant		4
STX7	ENST00000475879.1	n.60-252C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51302 AN: 151586 Hom.: 9358 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.338 AC: 51312 AN: 151674 Hom.: 9356 Cov.: 32 AF XY: 0.337 AC XY: 24933 AN XY: 74056

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.361

Alfa AF: 0.245 Hom.: 639

Bravo AF: 0.329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.66

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: rs2842884; hg19: chr6-132824979; COSMIC: COSV63399299;