Genetic Variant ENSG00000251661:n.115+2242G>T (chr11-320988-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000602429.2(ENSG00000251661):n.115+2242G>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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0830

Publications

11 publications found

Variant links:

Genes affected

ENSG00000251661 (HGNC:58185):

ENSG00000251661 links:

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]

IFITM3 links:

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ACMG classification

Classification was made for transcript

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFITM3	NM_021034.3 link	c.-175C>A		upstream_gene_variant		ENST00000399808.5	NP_066362.2	Q01628

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFITM3	ENST00000399808.5 link	c.-175C>A		upstream_gene_variant		1	NM_021034.3	ENSP00000382707.4		Q01628

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

581568

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

303938

African (AFR)

AF:

0.00

AC:

AN:

15956

American (AMR)

AF:

0.00

AC:

AN:

22106

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14508

East Asian (EAS)

AF:

0.00

AC:

AN:

30662

South Asian (SAS)

AF:

0.00

AC:

AN:

50278

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31520

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2192

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

384126

Other (OTH)

AF:

0.00

AC:

AN:

30220

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.1

(source)

DANN

Benign

0.76

PhyloP100

0.083

PromoterAI

-0.014

Neutral

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over