3-50292395-A-G

Position:

• chr3-50292395-A-G

Variant summary

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

The NM_006764.5(IFRD2):​c.-121T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 1,586,248 control chromosomes in the GnomAD database, including 391,136 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 0.77 (46402 hom., cov: 35)
  • Exomes 𝑓: 0.69 (344734 hom.)
• Consequence: IFRD2 NM_006764.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

IFRD2 (HGNC:5457): (interferon related developmental regulator 2) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFRD2	NM_006764.5	c.-121T>C		5_prime_UTR_variant	1/12	ENST00000417626.8	NP_006755.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFRD2	ENST00000417626.8	c.-121T>C		5_prime_UTR_variant	1/12	1	NM_006764.5	ENSP00000402849	P1

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117196 AN: 152126 Hom.: 46340 Cov.: 35

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.769

GnomAD3 exomes AF: 0.712 AC: 144573 AN: 203022 Hom.: 52803 AF XY: 0.691 AC XY: 78225 AN XY: 113164

Gnomad AFR exome AF: 0.949

Gnomad AMR exome AF: 0.867

Gnomad ASJ exome AF: 0.755

Gnomad EAS exome AF: 0.781

Gnomad SAS exome AF: 0.503

Gnomad FIN exome AF: 0.685

Gnomad NFE exome AF: 0.683

Gnomad OTH exome AF: 0.716

GnomAD4 exome AF: 0.690 AC: 989121 AN: 1434006 Hom.: 344734 Cov.: 74 AF XY: 0.683 AC XY: 487014 AN XY: 712626

Gnomad4 AFR exome AF: 0.954

Gnomad4 AMR exome AF: 0.859

Gnomad4 ASJ exome AF: 0.753

Gnomad4 EAS exome AF: 0.754

Gnomad4 SAS exome AF: 0.510

Gnomad4 FIN exome AF: 0.683

Gnomad4 NFE exome AF: 0.684

Gnomad4 OTH exome AF: 0.713

GnomAD4 genome AF: 0.771 AC: 117314 AN: 152242 Hom.: 46402 Cov.: 35 AF XY: 0.766 AC XY: 57005 AN XY: 74418

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.772

Alfa AF: 0.705 Hom.: 31505

Bravo AF: 0.797

Asia WGS AF: 0.622 AC: 2166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.9
DANN	Benign	0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6

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: rs1076872; hg19: chr3-50329826; COSMIC: COSV57112524; COSMIC: COSV57112524;