12-2788698-C-G

Variant names:

• chr12-2788698-C-G
• rs2968909
• ENST00000540093.2:n.411+8179G>C

Variant summary

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

The ENST00000540428.1(ITFG2-AS1):​n.300-1211G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,058 control chromosomes in the GnomAD database, including 10,545 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 0.32 (10545 hom., cov: 32)
• Consequence: ITFG2-AS1 ENST00000540428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 9 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITFG2-AS1	NR_146317.1		n.433+8179G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITFG2-AS1	ENST00000540093.2	TSL:3	n.411+8179G>C		intron	N/A
	ITFG2-AS1	ENST00000540428.1	TSL:2	n.300-1211G>C		intron	N/A
	ITFG2-AS1	ENST00000545526.2	TSL:2	n.732+7535G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48885 AN: 151940 Hom.: 10528 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.322 AC: 48950 AN: 152058 Hom.: 10545 Cov.: 32 AF XY: 0.326 AC XY: 24201 AN XY: 74310

African (AFR) AF: 0.598 AC: 24774 AN: 41458

American (AMR) AF: 0.286 AC: 4376 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 796 AN: 3472

East Asian (EAS) AF: 0.483 AC: 2493 AN: 5162

South Asian (SAS) AF: 0.386 AC: 1859 AN: 4812

European-Finnish (FIN) AF: 0.185 AC: 1952 AN: 10570

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11702 AN: 67986

Other (OTH) AF: 0.313 AC: 659 AN: 2108

Alfa AF: 0.116 Hom.: 191

Bravo AF: 0.338

Asia WGS AF: 0.448 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.49
PhyloP100		0.091

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2968909;

hg19: chr12-2897864;