rs7447927

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -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 (★★).

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

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STING1	NM_198282.4 link	c.144G>C	p.Val48Val	synonymous_variant	Exon 3 of 8	ENST00000330794.9	NP_938023.1	Q86WV6
STING1	NM_001301738.2 link	c.144G>C	p.Val48Val	synonymous_variant	Exon 3 of 7		NP_001288667.1	J3QTB1V5V0K2
STING1	NM_001367258.1 link	c.-130-219G>C		intron_variant	Intron 2 of 6		NP_001354187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STING1	ENST00000330794.9 link	c.144G>C	p.Val48Val	synonymous_variant	Exon 3 of 8	1	NM_198282.4	ENSP00000331288.4		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

GnomAD3 exomes

AF:

0.618

AC:

154729

AN:

250522

Hom.:

51269

AF XY:

0.636

AC XY:

86254

AN XY:

135622

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 SAS exome

AF:

0.678

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

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.491

Gnomad4 ASJ exome

AF:

0.633

Gnomad4 EAS exome

AF:

0.368

Gnomad4 SAS exome

AF:

0.679

Gnomad4 FIN exome

AF:

0.700

Gnomad4 NFE exome

AF:

0.737

Gnomad4 OTH exome

AF:

0.653

GnomAD4 genome

AF:

0.531

AC:

80719

AN:

152056

Hom.:

25808

Cov.:

AF XY:

0.529

AC XY:

39319

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.487

Gnomad4 ASJ

AF:

0.638

Gnomad4 EAS

AF:

0.378

Gnomad4 SAS

AF:

0.660

Gnomad4 FIN

AF:

0.693

Gnomad4 NFE

AF:

0.727

Gnomad4 OTH

AF:

0.551

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

Significance: Benign

Submissions summary: Benign:4Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Nov 12, 2023

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 80% of patients studied by a panel of primary immunodeficiencies. Number of patients: 77. Only high quality variants are reported. -

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

STING-associated vasculopathy with onset in infancy

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Other:1

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.91

DANN

Benign

0.35

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over