rs10757199

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNA7	NM_021057.2	c.-192C>A		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.-192C>A		upstream_gene_variant		6	NM_021057.2	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

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.194

Alfa AF: 0.180 Hom.: 494

Bravo AF: 0.202

Asia WGS AF: 0.250 AC: 867 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.075
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10757199; hg19: chr9-21202356;