Variant 2-191008827-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000361099.8(STAT1):c.273+136T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 895,406 control chromosomes in the GnomAD database, including 77,681 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.44 ( 15850 hom., cov: 33)

Exomes 𝑓: 0.40 ( 61831 hom. )

Consequence

STAT1
ENST00000361099.8 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.127

Variant links:

Genes affected

STAT1 (HGNC:11362): (signal transducer and activator of transcription 1) The protein encoded by this gene is a member of the STAT protein family. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. The protein encoded by this gene can be activated by various ligands including interferon-alpha, interferon-gamma, EGF, PDGF and IL6. This protein mediates the expression of a variety of genes, which is thought to be important for cell viability in response to different cell stimuli and pathogens. The protein plays an important role in immune responses to viral, fungal and mycobacterial pathogens. Mutations in this gene are associated with Immunodeficiency 31B, 31A, and 31C. [provided by RefSeq, Jun 2020]

STAT1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 2-191008827-A-T is Benign according to our data. Variant chr2-191008827-A-T is described in ClinVar as [Benign]. Clinvar id is 1258219.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAT1	NM_007315.4 linkuse as main transcript	c.273+136T>A		intron_variant		ENST00000361099.8	NP_009330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAT1	ENST00000361099.8 linkuse as main transcript	c.273+136T>A		intron_variant		1	NM_007315.4	ENSP00000354394	P4	P42224-1

Frequencies

GnomAD3 genomes

AF:

0.444

AC:

67432

AN:

151986

Hom.:

15824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.566

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.468

Gnomad EAS

AF:

0.721

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.374

Gnomad OTH

AF:

0.442

GnomAD4 exome

AF:

0.399

AC:

296427

AN:

743302

Hom.:

61831

AF XY:

0.399

AC XY:

153209

AN XY:

384116

show subpopulations

Gnomad4 AFR exome

AF:

0.576

Gnomad4 AMR exome

AF:

0.440

Gnomad4 ASJ exome

AF:

0.464

Gnomad4 EAS exome

AF:

0.709

Gnomad4 SAS exome

AF:

0.359

Gnomad4 FIN exome

AF:

0.331

Gnomad4 NFE exome

AF:

0.376

Gnomad4 OTH exome

AF:

0.429

GnomAD4 genome

AF:

0.444

AC:

67498

AN:

152104

Hom.:

15850

Cov.:

AF XY:

0.440

AC XY:

32722

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.565

Gnomad4 AMR

AF:

0.440

Gnomad4 ASJ

AF:

0.468

Gnomad4 EAS

AF:

0.720

Gnomad4 SAS

AF:

0.354

Gnomad4 FIN

AF:

0.332

Gnomad4 NFE

AF:

0.374

Gnomad4 OTH

AF:

0.447

Alfa

AF:

0.385

Hom.:

1422

Bravo

AF:

0.463

Asia WGS

AF:

0.549

AC:

1914

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.9

DANN

Benign

0.32

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

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