11-320988-G-T

Variant names:

• chr11-320988-G-T
• rs7479267
• ENST00000602429.2:n.115+2242G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000679433.1(IFITM3):​c.-22-216C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IFITM3 ENST00000679433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 11 publications found

Genes affected

IFITM3-AS1 (HGNC:58185):

IFITM3 (HGNC:5414): (interferon induced transmembrane protein 3) Interferon-induced transmembrane (IFITM) proteins are a family of interferon induced antiviral proteins. The family contains five members, including IFITM1, IFITM2 and IFITM3 and belong to the CD225 superfamily. The protein encoded by this gene restricts cellular entry by diverse viral pathogens, such as influenza A virus, Ebola virus and Sars-CoV-2. [provided by RefSeq, Nov 2021]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000679433.1. 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
	IFITM3	NM_021034.3	MANE Select	c.-175C>A		upstream_gene	N/A	NP_066362.2
	IFITM3	NR_049759.2		n.-128C>A		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFITM3-AS1	ENST00000602429.2	TSL:1	n.115+2242G>T		intron	N/A
	IFITM3	ENST00000526811.4	TSL:5	c.-22-216C>A		intron	N/A	ENSP00000432108.1
	IFITM3	ENST00000602735.2	TSL:5	c.-22-216C>A		intron	N/A	ENSP00000473544.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 581568 Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0 AN XY: 303938

African (AFR) AF: 0.00 AC: 0 AN: 15956

American (AMR) AF: 0.00 AC: 0 AN: 22106

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14508

East Asian (EAS) AF: 0.00 AC: 0 AN: 30662

South Asian (SAS) AF: 0.00 AC: 0 AN: 50278

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31520

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2192

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 384126

Other (OTH) AF: 0.00 AC: 0 AN: 30220

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.76
PhyloP100		0.083
PromoterAI		-0.014	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
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: rs7479267; hg19: chr11-320988;