Genetic Variant TGFB2-AS1:n.904_907delAGGA (chr1-218345080-GTCCT-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000687392.2(TGFB2-AS1):n.904_907delAGGA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 151,904 control chromosomes in the GnomAD database, including 56,670 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.86 ( 56658 hom., cov: 0)

Exomes 𝑓: 0.76 ( 12 hom. )

Consequence

TGFB2-AS1
ENST00000687392.2 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

Publications

0 publications found

Variant links:

Genes affected

TGFB2-AS1 (HGNC:50628): (TGFB2 antisense RNA 1 (head to head))

TGFB2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 1-218345080-GTCCT-G is Benign according to our data. Variant chr1-218345080-GTCCT-G is described in ClinVar as Benign. ClinVar VariationId is 1249061.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687392.2. 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
	TGFB2-AS1	NR_046268.1		n.290+91_290+94delAGGA		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
TGFB2-AS1	ENST00000687392.2		n.904_907delAGGA	non_coding_transcript_exon	Exon 1 of 1
TGFB2-AS1	ENST00000691401.2		n.721_724delAGGA	non_coding_transcript_exon	Exon 2 of 2
TGFB2-AS1	ENST00000414452.3	TSL:3	n.662+91_662+94delAGGA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.862

AC:

130798

AN:

151748

Hom.:

56614

Cov.:

show subpopulations

Gnomad AFR

AF:

0.944

Gnomad AMI

AF:

0.905

Gnomad AMR

AF:

0.827

Gnomad ASJ

AF:

0.826

Gnomad EAS

AF:

0.796

Gnomad SAS

AF:

0.707

Gnomad FIN

AF:

0.829

Gnomad MID

AF:

0.819

Gnomad NFE

AF:

0.843

Gnomad OTH

AF:

0.847

GnomAD4 exome

AF:

0.763

AC:

AN:

Hom.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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:

0.862

AC:

130896

AN:

151866

Hom.:

56658

Cov.:

AF XY:

0.857

AC XY:

63602

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.944

AC:

39164

AN:

41472

American (AMR)

AF:

0.826

AC:

12619

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.826

AC:

2863

AN:

3468

East Asian (EAS)

AF:

0.796

AC:

4086

AN:

5134

South Asian (SAS)

AF:

0.707

AC:

3409

AN:

4822

European-Finnish (FIN)

AF:

0.829

AC:

8710

AN:

10506

Middle Eastern (MID)

AF:

0.823

AC:

237

AN:

288

European-Non Finnish (NFE)

AF:

0.843

AC:

57204

AN:

67892

Other (OTH)

AF:

0.847

AC:

1780

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

908

1817

2725

3634

4542

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<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:

0.855

Hom.:

6778

Bravo

AF:

0.868

Asia WGS

AF:

0.757

AC:

2631

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over