ENST00000687762.2:n.677G>C

Variant names:

• chr21-33324196-C-G
• rs17875753
• ENST00000687762.2:n.677G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687762.2(ENSG00000289238):​n.677G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,720 control chromosomes in the GnomAD database, including 11,068 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 0.38 (11068 hom., cov: 32)
• Consequence: ENSG00000289238 ENST00000687762.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

ENSG00000289238 (HGNC:):

IFNAR1 (HGNC:5432): (interferon alpha and beta receptor subunit 1) The protein encoded by this gene is a type I membrane protein that forms one of the two chains of a receptor for interferons alpha and beta. Binding and activation of the receptor stimulates Janus protein kinases, which in turn phosphorylate several proteins, including STAT1 and STAT2. The protein belongs to the type II cytokine receptor family and functions as an antiviral factor. [provided by RefSeq, Jul 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNAR1	NM_001384504.1	c.-574C>G		upstream_gene_variant			NP_001371433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289238	ENST00000687762.2	n.677G>C		non_coding_transcript_exon_variant	Exon 1 of 1
IFNAR1	ENST00000652450.2	c.-574C>G		upstream_gene_variant				ENSP00000498654.1
IFNAR1	ENST00000700080.1	c.-714C>G		upstream_gene_variant				ENSP00000514785.1
IFNAR1	ENST00000700084.1	c.-656C>G		upstream_gene_variant				ENSP00000514786.1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57628 AN: 151602 Hom.: 11064 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.380 AC: 57647 AN: 151720 Hom.: 11068 Cov.: 32 AF XY: 0.379 AC XY: 28120 AN XY: 74150

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.401

Alfa AF: 0.393 Hom.: 1687

Bravo AF: 0.378

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17875753; hg19: chr21-34696501;