rs7046208

Variant names:

• chr9-21202409-G-A
• rs7046208
• NM_021057.2:c.-244C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-21202409-G-A
• chr9-21202409-G-T

Variant summary

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

The NM_021057.2(IFNA7):​c.-244C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 150,658 control chromosomes in the GnomAD database, including 8,098 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 0.32 (8098 hom., cov: 31)
• Consequence: IFNA7 NM_021057.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 2 publications found

Genes affected

IFNA7 (HGNC:5428): (interferon alpha 7) Predicted to enable cytokine activity and type I interferon receptor binding activity. Predicted to be involved in several processes, including B cell activation; lymphocyte activation involved in immune response; and positive regulation of peptidyl-serine phosphorylation of STAT protein. Predicted to be located in extracellular region. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNA7	NM_021057.2	c.-244C>T		upstream_gene_variant		ENST00000239347.3	NP_066401.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNA7	ENST00000239347.3	c.-244C>T		upstream_gene_variant		6	NM_021057.2	ENSP00000239347.3

Frequencies

GnomAD3 genomes AF: 0.324 AC: 48843 AN: 150540 Hom.: 8095 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.317

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.324 AC: 48866 AN: 150658 Hom.: 8098 Cov.: 31 AF XY: 0.327 AC XY: 24056 AN XY: 73500

African (AFR) AF: 0.268 AC: 10962 AN: 40892

American (AMR) AF: 0.310 AC: 4690 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1117 AN: 3458

East Asian (EAS) AF: 0.334 AC: 1708 AN: 5110

South Asian (SAS) AF: 0.504 AC: 2413 AN: 4786

European-Finnish (FIN) AF: 0.348 AC: 3581 AN: 10300

Middle Eastern (MID) AF: 0.334 AC: 97 AN: 290

European-Non Finnish (NFE) AF: 0.343 AC: 23211 AN: 67716

Other (OTH) AF: 0.343 AC: 719 AN: 2096

Alfa AF: 0.318 Hom.: 945

Bravo AF: 0.317

Asia WGS AF: 0.436 AC: 1517 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.42
PhyloP100		-1.7
PromoterAI		-0.0098	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7046208; hg19: chr9-21202408; COSMIC: COSV53332222;