chr12-2776963-C-T

Variant names:

• chr12-2776963-C-T
• rs4409904
• ENST00000540093.2:n.412-5056G>A

Variant summary

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

The ENST00000540093.2(ITFG2-AS1):​n.412-5056G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,216 control chromosomes in the GnomAD database, including 1,112 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 0.12 (1112 hom., cov: 32)
• Consequence: ITFG2-AS1 ENST00000540093.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540093.2. 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.434-5056G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITFG2-AS1	ENST00000540093.2	TSL:3	n.412-5056G>A		intron	N/A
	ITFG2-AS1	ENST00000545526.2	TSL:2	n.733-5056G>A		intron	N/A
	ITFG2-AS1	ENST00000636122.1	TSL:5	n.193-5056G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18110 AN: 152098 Hom.: 1114 Cov.: 32

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.0947

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0692

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.119 AC: 18107 AN: 152216 Hom.: 1112 Cov.: 32 AF XY: 0.115 AC XY: 8590 AN XY: 74418

African (AFR) AF: 0.0994 AC: 4130 AN: 41540

American (AMR) AF: 0.100 AC: 1530 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3472

East Asian (EAS) AF: 0.102 AC: 526 AN: 5172

South Asian (SAS) AF: 0.0691 AC: 333 AN: 4822

European-Finnish (FIN) AF: 0.0988 AC: 1047 AN: 10600

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9568 AN: 67994

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.132 Hom.: 2233

Bravo AF: 0.120

Asia WGS AF: 0.0680 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.99
DANN	Benign	0.43
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs4409904; hg19: chr12-2886129;