rs7447927

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_198282.4(STING1):c.144G>C(p.Val48Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 1,613,522 control chromosomes in the GnomAD database, including 389,177 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. V48V) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.53 ( 25808 hom., cov: 31)

Exomes 𝑓: 0.70 ( 363369 hom. )

Consequence

STING1
NM_198282.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4O:1

Conservation

PhyloP100: -0.115

Publications

45 publications found

Variant links:

Genes affected

STING1 (HGNC:27962): (stimulator of interferon response cGAMP interactor 1) This gene encodes a five transmembrane protein that functions as a major regulator of the innate immune response to viral and bacterial infections. The encoded protein is a pattern recognition receptor that detects cytosolic nucleic acids and transmits signals that activate type I interferon responses. The encoded protein has also been shown to play a role in apoptotic signaling by associating with type II major histocompatibility complex. Mutations in this gene are the cause of infantile-onset STING-associated vasculopathy. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2014]

STING1 Gene-Disease associations (from GenCC):

STING-associated vasculopathy with onset in infancy
Inheritance: AD, AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, PanelApp Australia, Orphanet
familial chilblain lupus
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

STING1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 5-139481561-C-G is Benign according to our data. Variant chr5-139481561-C-G is described in ClinVar as Benign. ClinVar VariationId is 403551.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198282.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
STING1	NM_198282.4	MANE Select	c.144G>C	p.Val48Val	synonymous	Exon 3 of 8	NP_938023.1	Q86WV6
STING1	NM_001301738.2		c.144G>C	p.Val48Val	synonymous	Exon 3 of 7	NP_001288667.1	J3QTB1
STING1	NM_001367258.1		c.-130-219G>C		intron	N/A	NP_001354187.1	A0A494C0W5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
STING1	ENST00000330794.9	TSL:1 MANE Select	c.144G>C	p.Val48Val	synonymous	Exon 3 of 8	ENSP00000331288.4	Q86WV6
STING1	ENST00000512606.6	TSL:1	n.245G>C		non_coding_transcript_exon	Exon 2 of 6
STING1	ENST00000651699.1		c.144G>C	p.Val48Val	synonymous	Exon 2 of 7	ENSP00000499166.1	Q86WV6

Frequencies

GnomAD3 genomes

AF:

0.531

AC:

80730

AN:

151938

Hom.:

25818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.659

Gnomad AMR

AF:

0.488

Gnomad ASJ

AF:

0.638

Gnomad EAS

AF:

0.378

Gnomad SAS

AF:

0.660

Gnomad FIN

AF:

0.693

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.727

Gnomad OTH

AF:

0.554

GnomAD2 exomes

AF:

0.618

AC:

154729

AN:

250522

AF XY:

0.636

show subpopulations

Gnomad AFR exome

AF:

0.164

Gnomad AMR exome

AF:

0.492

Gnomad ASJ exome

AF:

0.636

Gnomad EAS exome

AF:

0.368

Gnomad FIN exome

AF:

0.704

Gnomad NFE exome

AF:

0.725

Gnomad OTH exome

AF:

0.653

GnomAD4 exome

AF:

0.696

AC:

1016618

AN:

1461466

Hom.:

363369

Cov.:

AF XY:

0.698

AC XY:

507161

AN XY:

727054

show subpopulations

African (AFR)

AF:

0.163

AC:

5460

AN:

33472

American (AMR)

AF:

0.491

AC:

21967

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.633

AC:

16543

AN:

26128

East Asian (EAS)

AF:

0.368

AC:

14623

AN:

39686

South Asian (SAS)

AF:

0.679

AC:

58581

AN:

86258

European-Finnish (FIN)

AF:

0.700

AC:

37237

AN:

53198

Middle Eastern (MID)

AF:

0.613

AC:

3537

AN:

5768

European-Non Finnish (NFE)

AF:

0.737

AC:

819220

AN:

1111874

Other (OTH)

AF:

0.653

AC:

39450

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

16483

32966

49450

65933

82416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19804

39608

59412

79216

99020

<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:

0.531

AC:

80719

AN:

152056

Hom.:

25808

Cov.:

AF XY:

0.529

AC XY:

39319

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.175

AC:

7255

AN:

41498

American (AMR)

AF:

0.487

AC:

7444

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.638

AC:

2212

AN:

3468

East Asian (EAS)

AF:

0.378

AC:

1952

AN:

5168

South Asian (SAS)

AF:

0.660

AC:

3182

AN:

4822

European-Finnish (FIN)

AF:

0.693

AC:

7338

AN:

10590

Middle Eastern (MID)

AF:

0.578

AC:

170

AN:

294

European-Non Finnish (NFE)

AF:

0.727

AC:

49403

AN:

67916

Other (OTH)

AF:

0.551

AC:

1162

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1501

3002

4503

6004

7505

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

684

1368

2052

2736

3420

<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:

0.666

Hom.:

11351

Bravo

AF:

0.498

Asia WGS

AF:

0.469

AC:

1630

AN:

3478

EpiCase

AF:

0.711

EpiControl

AF:

0.708

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (2)

STING-associated vasculopathy with onset in infancy (2)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.91

(source)

DANN

Benign

0.35

PhyloP100

-0.12

PromoterAI

-0.012

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.22

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.22

Position offset: -11

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over