2-190998211-A-T

Variant names:

• chr2-190998211-A-T
• rs45459703
• NM_007315.4:c.633+6T>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The NM_007315.4(STAT1):​c.633+6T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00435 in 1,610,038 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0032 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0045 (24 hom.)
• Consequence: STAT1 NM_007315.4 splice_region, intron
• Scores: Splicing: ADA: 0.001653
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:6
• Conservation: PhyloP100: 0.194

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]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 2-190998211-A-T is Benign according to our data. Variant chr2-190998211-A-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 333289.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1, Benign=2}. Variant chr2-190998211-A-T is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00324 (494/152336) while in subpopulation NFE AF = 0.00516 (351/68028). AF 95% confidence interval is 0.00471. There are 2 homozygotes in GnomAd4. There are 230 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 2 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAT1	NM_007315.4	c.633+6T>A		splice_region_variant, intron_variant	Intron 8 of 24	ENST00000361099.8	NP_009330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAT1	ENST00000361099.8	c.633+6T>A		splice_region_variant, intron_variant	Intron 8 of 24	1	NM_007315.4	ENSP00000354394.4

Frequencies

GnomAD3 genomes AF: 0.00325 AC: 494 AN: 152218 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.000869

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00452

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000827

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00516

Gnomad OTH AF: 0.00239

GnomAD2 exomes AF: 0.00307 AC: 772 AN: 251186 AF XY: 0.00298

Gnomad AFR exome AF: 0.00105

Gnomad AMR exome AF: 0.00280

Gnomad ASJ exome AF: 0.00308

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00149

Gnomad NFE exome AF: 0.00491

Gnomad OTH exome AF: 0.00326

GnomAD4 exome AF: 0.00447 AC: 6515 AN: 1457702 Hom.: 24 Cov.: 30 AF XY: 0.00440 AC XY: 3190 AN XY: 725486

Gnomad4 AFR exome AF: 0.000987 AC: 33 AN: 33420

Gnomad4 AMR exome AF: 0.00262 AC: 117 AN: 44722

Gnomad4 ASJ exome AF: 0.00287 AC: 75 AN: 26096

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39646

Gnomad4 SAS exome AF: 0.000638 AC: 55 AN: 86164

Gnomad4 FIN exome AF: 0.00160 AC: 85 AN: 53164

Gnomad4 NFE exome AF: 0.00537 AC: 5953 AN: 1108480

Gnomad4 Remaining exome AF: 0.00319 AC: 192 AN: 60264

GnomAD4 genome AF: 0.00324 AC: 494 AN: 152336 Hom.: 2 Cov.: 32 AF XY: 0.00309 AC XY: 230 AN XY: 74500

Gnomad4 AFR AF: 0.000866 AC: 0.000866092 AN: 0.000866092

Gnomad4 AMR AF: 0.00451 AC: 0.00451039 AN: 0.00451039

Gnomad4 ASJ AF: 0.00375 AC: 0.0037464 AN: 0.0037464

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000828 AC: 0.000827815 AN: 0.000827815

Gnomad4 FIN AF: 0.00151 AC: 0.00150517 AN: 0.00150517

Gnomad4 NFE AF: 0.00516 AC: 0.00515964 AN: 0.00515964

Gnomad4 OTH AF: 0.00236 AC: 0.00236295 AN: 0.00236295

Alfa AF: 0.00446 Hom.: 0

Bravo AF: 0.00322

EpiCase AF: 0.00420

EpiControl AF: 0.00504

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:6

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Benign:3

-

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Nov 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

STAT1: BP4, BS2 -

Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency Uncertain:1 Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Mar 22, 2018

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -

STAT1-related disorder Benign:1

Apr 01, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Immunodeficiency 31B;C3279990:Autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome;C4013950:Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency Benign:1

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	15
DANN	Benign	0.80
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0017
dbscSNV1_RF	Benign	0.072
SpliceAI score (max)		0.060		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

Other links and lift over

dbSNP: rs45459703; hg19: chr2-191862937;