6-132493244-C-T

Variant names:

• chr6-132493244-C-T
• rs2842892
• NM_003569.3:c.85+10202G>A

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+10202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,154 control chromosomes in the GnomAD database, including 58,717 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 0.88 (58717 hom., cov: 32)
• Consequence: STX7 NM_003569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STX7	NM_003569.3	c.85+10202G>A		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+10202G>A		intron_variant	Intron 2 of 9	1	NM_003569.3	ENSP00000356918.1
STX7	ENST00000367937.4	c.85+10202G>A		intron_variant	Intron 2 of 9	5		ENSP00000356914.4
STX7	ENST00000448348.3	n.147+10202G>A		intron_variant	Intron 2 of 6	4
STX7	ENST00000475879.1	n.202+10202G>A		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133472 AN: 152038 Hom.: 58680 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.878 AC: 133558 AN: 152154 Hom.: 58717 Cov.: 32 AF XY: 0.875 AC XY: 65065 AN XY: 74378

African (AFR) AF: 0.899 AC: 37308 AN: 41504

American (AMR) AF: 0.816 AC: 12475 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3225 AN: 3472

East Asian (EAS) AF: 0.924 AC: 4797 AN: 5190

South Asian (SAS) AF: 0.891 AC: 4297 AN: 4824

European-Finnish (FIN) AF: 0.823 AC: 8694 AN: 10566

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59733 AN: 67990

Other (OTH) AF: 0.901 AC: 1902 AN: 2110

Alfa AF: 0.855 Hom.: 5634

Bravo AF: 0.879

Asia WGS AF: 0.890 AC: 3097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.19
PhyloP100		-1.3
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: rs2842892; hg19: chr6-132814383;