11-320988-G-A

Position:

• chr11-320988-G-A

Variant summary

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

The ENST00000602429.1(ENSG00000251661):​n.94+2242G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 145,174 control chromosomes in the GnomAD database, including 15,272 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 0.51 (15272 hom., cov: 32)
  • Exomes 𝑓: 0.56 (83596 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000602429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376505	XR_007062535.1	n.287+2242G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000602429.1	n.94+2242G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 73445 AN: 145074 Hom.: 15270 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.447

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.489

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.561 AC: 324880 AN: 578690 Hom.: 83596 Cov.: 8 AF XY: 0.559 AC XY: 168991 AN XY: 302434

Gnomad4 AFR exome AF: 0.396

Gnomad4 AMR exome AF: 0.604

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.620

Gnomad4 SAS exome AF: 0.505

Gnomad4 FIN exome AF: 0.634

Gnomad4 NFE exome AF: 0.566

Gnomad4 OTH exome AF: 0.551

GnomAD4 genome AF: 0.506 AC: 73485 AN: 145174 Hom.: 15272 Cov.: 32 AF XY: 0.508 AC XY: 35925 AN XY: 70724

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.490

Alfa AF: 0.407 Hom.: 700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.5
DANN	Benign	0.76

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: rs7479267; hg19: chr11-320988; COSMIC: COSV67706779; COSMIC: COSV67706779;