Genetic Variant ITFG2-AS1:n.412-1471G>A (chr12-2773378-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.811

Publications

7 publications found

Variant links:

Genes affected

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

ITFG2-AS1 links:

ENSG00000255669 (HGNC:):

ENSG00000255669 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITFG2-AS1	NR_146317.1 link	n.434-1471G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ITFG2-AS1	ENST00000540093.2 link	n.412-1471G>A	intron_variant	Intron 2 of 3	3
ITFG2-AS1	ENST00000545526.2 link	n.733-1471G>A	intron_variant	Intron 4 of 7	2
ITFG2-AS1	ENST00000636122.1 link	n.193-1471G>A	intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113693

AN:

151852

Hom.:

42727

Cov.:

show subpopulations

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.:

AF XY:

0.811

AC XY:

AN XY:

106

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.917

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.817

AC:

AN:

120

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.587

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.749

AC:

113755

AN:

151972

Hom.:

42740

Cov.:

AF XY:

0.747

AC XY:

55506

AN XY:

74296

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1431

2862

4294

5725

7156

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

854

1708

2562

3416

4270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

7.4

(source)

DANN

Benign

0.55

PhyloP100

0.81

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over