NM_021057.2:c.-192C>A

Variant names:

• chr9-21202357-G-T
• rs10757199
• NM_021057.2:c.-192C>A

Variant summary

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

The NM_021057.2(IFNA7):​c.-192C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,518 control chromosomes in the GnomAD database, including 3,212 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 0.20 (3212 hom., cov: 31)
• Consequence: IFNA7 NM_021057.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.17
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021057.2. 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
	IFNA7	NM_021057.2	MANE Select	c.-192C>A		upstream_gene	N/A	NP_066401.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNA7	ENST00000239347.3	TSL:6 MANE Select	c.-192C>A		upstream_gene	N/A	ENSP00000239347.3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29677 AN: 151400 Hom.: 3211 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.196 AC: 29700 AN: 151518 Hom.: 3212 Cov.: 31 AF XY: 0.197 AC XY: 14592 AN XY: 74056

African (AFR) AF: 0.201 AC: 8291 AN: 41198

American (AMR) AF: 0.247 AC: 3753 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3464

East Asian (EAS) AF: 0.416 AC: 2140 AN: 5146

South Asian (SAS) AF: 0.120 AC: 577 AN: 4804

European-Finnish (FIN) AF: 0.197 AC: 2067 AN: 10502

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11593 AN: 67906

Other (OTH) AF: 0.194 AC: 408 AN: 2106

Alfa AF: 0.179 Hom.: 828

Bravo AF: 0.202

Asia WGS AF: 0.250 AC: 867 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.075
DANN	Benign	0.40
PhyloP100		-6.2
PromoterAI		-0.0016	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10757199; hg19: chr9-21202356;