rs3888188

chr11-321017-A-Cchr11-321017-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000602429.1(ENSG00000251661):n.94+2271A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.26 (1245 hom., cov: 32)
  • Exomes 𝑓: 0.22 (6888 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000602429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

(HGNC:):

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376505	XR_007062535.1	n.287+2271A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000602429.1	n.94+2271A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 27387 AN: 107176 Hom.: 1247 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.220 AC: 72919 AN: 330746 Hom.: 6888 Cov.: 5 AF XY: 0.226 AC XY: 39211 AN XY: 173534

Gnomad4 AFR exome AF: 0.242

Gnomad4 AMR exome AF: 0.314

Gnomad4 ASJ exome AF: 0.157

Gnomad4 EAS exome AF: 0.693

Gnomad4 SAS exome AF: 0.334

Gnomad4 FIN exome AF: 0.157

Gnomad4 NFE exome AF: 0.142

Gnomad4 OTH exome AF: 0.207

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.256 AC: 27412 AN: 107254 Hom.: 1245 Cov.: 32 AF XY: 0.263 AC XY: 13888 AN XY: 52714

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.265

Alfa AF: 0.220 Hom.: 58

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	1.0
Dann	Benign	0.86

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

LitVar

Other links and lift over

dbSNP: rs3888188; hg19: chr11-321017; COSMIC: COSV67707159; COSMIC: COSV67707159;