rs7849623

Variant names:

• chr9-21191464-G-A
• rs7849623
• ENST00000448683.1:n.-220C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-21191464-G-A
• chr9-21191464-G-T

Variant summary

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

The ENST00000448683.1(IFNWP9):​n.-220C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,544 control chromosomes in the GnomAD database, including 4,697 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 0.23 (4697 hom., cov: 31)
• Consequence: IFNWP9 ENST00000448683.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.07

Genes affected

IFNWP9 (HGNC:5455): (interferon omega 1 pseudogene 9)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNWP9	ENST00000448683.1	n.-220C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35154 AN: 151426 Hom.: 4685 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.232 AC: 35219 AN: 151544 Hom.: 4697 Cov.: 31 AF XY: 0.234 AC XY: 17360 AN XY: 74050

African (AFR) AF: 0.301 AC: 12396 AN: 41210

American (AMR) AF: 0.274 AC: 4179 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3464

East Asian (EAS) AF: 0.518 AC: 2659 AN: 5130

South Asian (SAS) AF: 0.181 AC: 865 AN: 4790

European-Finnish (FIN) AF: 0.201 AC: 2124 AN: 10556

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11662 AN: 67866

Other (OTH) AF: 0.217 AC: 456 AN: 2098

Alfa AF: 0.182 Hom.: 1416

Bravo AF: 0.242

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.78
DANN	Benign	0.19
PhyloP100		-4.1

Splicing

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

Publications

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Other links and lift over

dbSNP: rs7849623; hg19: chr9-21191463;