12-2792404-T-C

Variant names:

• chr12-2792404-T-C
• rs3759411
• ENST00000540093.2:n.411+4473A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000540428.1(ITFG2-AS1):​n.299+1593A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 151,936 control chromosomes in the GnomAD database, including 1,745 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 0.14 (1745 hom., cov: 31)
• Consequence: ITFG2-AS1 ENST00000540428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 4 publications found

Genes affected

ITFG2-AS1 (HGNC:53128): (ITFG2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540428.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITFG2-AS1	NR_146317.1		n.433+4473A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITFG2-AS1	ENST00000540093.2	TSL:3	n.411+4473A>G		intron	N/A
	ITFG2-AS1	ENST00000540428.1	TSL:2	n.299+1593A>G		intron	N/A
	ITFG2-AS1	ENST00000545526.2	TSL:2	n.732+3829A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21640 AN: 151816 Hom.: 1752 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.142 AC: 21634 AN: 151936 Hom.: 1745 Cov.: 31 AF XY: 0.148 AC XY: 10985 AN XY: 74244

African (AFR) AF: 0.125 AC: 5186 AN: 41444

American (AMR) AF: 0.133 AC: 2030 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1411 AN: 5126

South Asian (SAS) AF: 0.313 AC: 1505 AN: 4810

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10542

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8684 AN: 67982

Other (OTH) AF: 0.151 AC: 318 AN: 2112

Alfa AF: 0.137 Hom.: 1499

Bravo AF: 0.138

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.63
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs3759411; hg19: chr12-2901570;