11-321017-A-T

Variant names:

• chr11-321017-A-T
• rs3888188
• ENST00000602429.2:n.115+2271A>T

Variant summary

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

The ENST00000602429.2(ENSG00000251661):​n.115+2271A>T 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: ENSG00000251661 ENST00000602429.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 14 publications found

Genes affected

ENSG00000251661 (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=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFITM3	NM_021034.3	c.-204T>A		upstream_gene_variant		ENST00000399808.5	NP_066362.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFITM3	ENST00000399808.5	c.-204T>A		upstream_gene_variant		1	NM_021034.3	ENSP00000382707.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 396998 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 208836

African (AFR) AF: 0.00 AC: 0 AN: 10944

American (AMR) AF: 0.00 AC: 0 AN: 15876

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10894

East Asian (EAS) AF: 0.00 AC: 0 AN: 29310

South Asian (SAS) AF: 0.00 AC: 0 AN: 39798

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23020

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1648

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 243512

Other (OTH) AF: 0.00 AC: 0 AN: 21996

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 58

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.97
DANN	Benign	0.87
PhyloP100		-2.0
PromoterAI		-0.0018	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: rs3888188; hg19: chr11-321017;