12-2773378-C-T

Position:

• chr12-2773378-C-T

Variant summary

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

The ENST00000540093.2(ITFG2-AS1):​n.412-1471G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,122 control chromosomes in the GnomAD database, including 42,792 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 0.75 (42740 hom., cov: 31)
  • Exomes 𝑓: 0.83 (52 hom.)
• Consequence: ITFG2-AS1 ENST00000540093.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.811

Genes affected

ITFG2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITFG2-AS1	NR_146317.1	n.434-1471G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITFG2-AS1	ENST00000540093.2	n.412-1471G>A		intron_variant		3
ITFG2-AS1	ENST00000636122.1	n.193-1471G>A		intron_variant		5
ENSG00000255669	ENST00000637160.1	n.255-96G>A		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113693 AN: 151852 Hom.: 42727 Cov.: 31

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.731

GnomAD4 exome AF: 0.833 AC: 125 AN: 150 Hom.: 52 AF XY: 0.811 AC XY: 86 AN XY: 106

Gnomad4 AFR exome AF: 0.667

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.917

Gnomad4 NFE exome AF: 0.817

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.749 AC: 113755 AN: 151972 Hom.: 42740 Cov.: 31 AF XY: 0.747 AC XY: 55506 AN XY: 74296

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.726

Alfa AF: 0.766 Hom.: 76318

Bravo AF: 0.746

Asia WGS AF: 0.678 AC: 2358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.4
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10848704; hg19: chr12-2882544;