chr2-190986040-C-A

Variant names:

• chr2-190986040-C-A
• rs2280232
• NM_007315.4:c.1222-380G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007315.4(STAT1):​c.1222-380G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,034 control chromosomes in the GnomAD database, including 41,462 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 0.74 (41462 hom., cov: 32)
• Consequence: STAT1 NM_007315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 22 publications found

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 Gene-Disease associations (from GenCC):

• autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Illumina, Orphanet
• immunodeficiency 31B

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet
• Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency

  Inheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007315.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAT1	NM_007315.4	MANE Select	c.1222-380G>T		intron	N/A	NP_009330.1
	STAT1	NM_001384891.1		c.1258-380G>T		intron	N/A	NP_001371820.1
	STAT1	NM_001384886.1		c.1222-380G>T		intron	N/A	NP_001371815.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAT1	ENST00000361099.8	TSL:1 MANE Select	c.1222-380G>T		intron	N/A	ENSP00000354394.4
	STAT1	ENST00000409465.5	TSL:1	c.1222-380G>T		intron	N/A	ENSP00000386244.1
	STAT1	ENST00000392322.7	TSL:1	c.1222-380G>T		intron	N/A	ENSP00000376136.3

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111975 AN: 151916 Hom.: 41447 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.705

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.737 AC: 112030 AN: 152034 Hom.: 41462 Cov.: 32 AF XY: 0.739 AC XY: 54890 AN XY: 74270

African (AFR) AF: 0.698 AC: 28957 AN: 41460

American (AMR) AF: 0.697 AC: 10643 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2284 AN: 3470

East Asian (EAS) AF: 0.833 AC: 4285 AN: 5146

South Asian (SAS) AF: 0.708 AC: 3407 AN: 4812

European-Finnish (FIN) AF: 0.817 AC: 8648 AN: 10588

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51513 AN: 67972

Other (OTH) AF: 0.708 AC: 1493 AN: 2110

Alfa AF: 0.738 Hom.: 75252

Bravo AF: 0.722

Asia WGS AF: 0.764 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.79
DANN	Benign	0.53
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2280232; hg19: chr2-191850766;