12-2773378-C-T

Variant names:

• chr12-2773378-C-T
• rs10848704
• ENST00000540093.2:n.412-1471G>A

Variant summary

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

The ENST00000545526.2(ITFG2-AS1):​n.733-1471G>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 ENST00000545526.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.811
• Publications: 7 publications found

Genes affected

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

ENSG00000255669 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000545526.2. 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.434-1471G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITFG2-AS1	ENST00000540093.2	TSL:3	n.412-1471G>A		intron	N/A
	ITFG2-AS1	ENST00000545526.2	TSL:2	n.733-1471G>A		intron	N/A
	ITFG2-AS1	ENST00000636122.1	TSL:5	n.193-1471G>A		intron	N/A

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

African (AFR) AF: 0.667 AC: 4 AN: 6

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.917 AC: 11 AN: 12

Middle Eastern (MID) AF: 1.00 AC: 6 AN: 6

European-Non Finnish (NFE) AF: 0.817 AC: 98 AN: 120

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.702 AC: 29076 AN: 41420

American (AMR) AF: 0.765 AC: 11683 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2554 AN: 3472

East Asian (EAS) AF: 0.730 AC: 3760 AN: 5150

South Asian (SAS) AF: 0.655 AC: 3162 AN: 4824

European-Finnish (FIN) AF: 0.797 AC: 8424 AN: 10576

Middle Eastern (MID) AF: 0.628 AC: 182 AN: 290

European-Non Finnish (NFE) AF: 0.776 AC: 52751 AN: 67950

Other (OTH) AF: 0.726 AC: 1528 AN: 2104

Alfa AF: 0.764 Hom.: 178082

Bravo AF: 0.746

Asia WGS AF: 0.678 AC: 2358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.4
DANN	Benign	0.55
PhyloP100		0.81

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: rs10848704;

hg19: chr12-2882544;