Genetic Variant NM_003569.3:c.611-10T>G (chr6-132464085-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003569.3(STX7):c.611-10T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,610,954 control chromosomes in the GnomAD database, including 38,582 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 0.21 ( 3333 hom., cov: 32)

Exomes 𝑓: 0.22 ( 35249 hom. )

Consequence

STX7
NM_003569.3 intron

Scores

Splicing: ADA: 0.1601

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.34

Publications

8 publications found

Variant links:

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]

STX7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STX7	NM_003569.3 link	c.611-10T>G		intron_variant	Intron 8 of 9	ENST00000367941.7	NP_003560.2	O15400-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STX7	ENST00000367941.7 link	c.611-10T>G		intron_variant	Intron 8 of 9	1	NM_003569.3	ENSP00000356918.1		O15400-1
STX7	ENST00000367937.4 link	c.611-10T>G		intron_variant	Intron 8 of 9	5		ENSP00000356914.4		O15400-2

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31552

AN:

152046

Hom.:

3329

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.249

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.209

GnomAD2 exomes

AF:

0.213

AC:

53406

AN:

250322

AF XY:

0.216

show subpopulations

Gnomad AFR exome

AF:

0.213

Gnomad AMR exome

AF:

0.223

Gnomad ASJ exome

AF:

0.256

Gnomad EAS exome

AF:

0.142

Gnomad FIN exome

AF:

0.171

Gnomad NFE exome

AF:

0.210

Gnomad OTH exome

AF:

0.231

GnomAD4 exome

AF:

0.218

AC:

318663

AN:

1458790

Hom.:

35249

Cov.:

AF XY:

0.220

AC XY:

159865

AN XY:

725900

show subpopulations

African (AFR)

AF:

0.216

AC:

7221

AN:

33418

American (AMR)

AF:

0.220

AC:

9837

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

6628

AN:

26104

East Asian (EAS)

AF:

0.181

AC:

7192

AN:

39666

South Asian (SAS)

AF:

0.267

AC:

23032

AN:

86154

European-Finnish (FIN)

AF:

0.167

AC:

8875

AN:

53082

Middle Eastern (MID)

AF:

0.278

AC:

1601

AN:

5756

European-Non Finnish (NFE)

AF:

0.217

AC:

240794

AN:

1109620

Other (OTH)

AF:

0.224

AC:

13483

AN:

60278

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

12183

24366

36548

48731

60914

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8486

16972

25458

33944

42430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.207

AC:

31556

AN:

152164

Hom.:

3333

Cov.:

AF XY:

0.206

AC XY:

15295

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.214

AC:

8904

AN:

41516

American (AMR)

AF:

0.186

AC:

2850

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

864

AN:

3470

East Asian (EAS)

AF:

0.154

AC:

795

AN:

5178

South Asian (SAS)

AF:

0.266

AC:

1281

AN:

4818

European-Finnish (FIN)

AF:

0.167

AC:

1775

AN:

10598

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.212

AC:

14401

AN:

67992

Other (OTH)

AF:

0.207

AC:

436

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1255

2509

3764

5018

6273

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.213

Hom.:

1855

Bravo

AF:

0.211

Asia WGS

AF:

0.245

AC:

853

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.65

PhyloP100

3.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.16

dbscSNV1_RF

Benign

0.49

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over