rs1333973

Variant names:

• chr1-78628396-T-A
• rs1333973
• ENST00000486882.5:n.2727T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-78628396-T-A
• chr1-78628396-T-C
• chr1-78628396-T-G

Variant summary

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

The ENST00000486882.5(IFI44L):​n.2727T>A 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 0.348 in 1,482,864 control chromosomes in the GnomAD database, including 95,164 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 0.35 (9790 hom., cov: 32)
  • Exomes 𝑓: 0.35 (85374 hom.)
• Consequence: IFI44L ENST00000486882.5 non_coding_transcript_exon
• Scores: Splicing: ADA: 0.00001621
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684
• Publications: 28 publications found

Genes affected

IFI44L (HGNC:17817): (interferon induced protein 44 like) Predicted to enable GTP binding activity. Involved in defense response to virus. Predicted to be located in cytoplasm. [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=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486882.5. 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
	IFI44L	NM_006820.4	MANE Select	c.478+3T>A		splice_region intron	N/A	NP_006811.2
	IFI44L	NM_001375646.1		c.478+3T>A		splice_region intron	N/A	NP_001362575.1
	IFI44L	NM_001375647.1		c.-296-555T>A		intron	N/A	NP_001362576.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFI44L	ENST00000486882.5	TSL:1	n.2727T>A		non_coding_transcript_exon	Exon 1 of 7
	IFI44L	ENST00000370751.10	TSL:1 MANE Select	c.478+3T>A		splice_region intron	N/A	ENSP00000359787.4
	IFI44L	ENST00000459784.6	TSL:3	c.-296-555T>A		intron	N/A	ENSP00000506096.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52724 AN: 151816 Hom.: 9781 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.371

GnomAD2 exomes AF: 0.381 AC: 77914 AN: 204398 AF XY: 0.381

Gnomad AFR exome AF: 0.306

Gnomad AMR exome AF: 0.362

Gnomad ASJ exome AF: 0.330

Gnomad EAS exome AF: 0.756

Gnomad FIN exome AF: 0.398

Gnomad NFE exome AF: 0.327

Gnomad OTH exome AF: 0.373

GnomAD4 exome AF: 0.348 AC: 462716 AN: 1330932 Hom.: 85374 Cov.: 22 AF XY: 0.349 AC XY: 231604 AN XY: 663152

African (AFR) AF: 0.305 AC: 8863 AN: 29026

American (AMR) AF: 0.354 AC: 11697 AN: 33026

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 7289 AN: 22560

East Asian (EAS) AF: 0.784 AC: 30428 AN: 38794

South Asian (SAS) AF: 0.417 AC: 31111 AN: 74648

European-Finnish (FIN) AF: 0.388 AC: 19710 AN: 50744

Middle Eastern (MID) AF: 0.372 AC: 1551 AN: 4174

European-Non Finnish (NFE) AF: 0.324 AC: 331568 AN: 1022660

Other (OTH) AF: 0.371 AC: 20499 AN: 55300

GnomAD4 genome AF: 0.347 AC: 52778 AN: 151932 Hom.: 9790 Cov.: 32 AF XY: 0.354 AC XY: 26252 AN XY: 74254

African (AFR) AF: 0.310 AC: 12830 AN: 41448

American (AMR) AF: 0.331 AC: 5059 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3468

East Asian (EAS) AF: 0.761 AC: 3928 AN: 5164

South Asian (SAS) AF: 0.425 AC: 2052 AN: 4824

European-Finnish (FIN) AF: 0.395 AC: 4162 AN: 10526

Middle Eastern (MID) AF: 0.348 AC: 101 AN: 290

European-Non Finnish (NFE) AF: 0.331 AC: 22510 AN: 67924

Other (OTH) AF: 0.374 AC: 787 AN: 2104

Alfa AF: 0.335 Hom.: 1688

Bravo AF: 0.341

Asia WGS AF: 0.561 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.53
PhyloP100		0.68
PromoterAI		0.052	Neutral
Mutation Taster		=86/14	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000016
dbscSNV1_RF	Benign	0.0060
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1333973; hg19: chr1-79094081;