Variant 1-218345080-GTCCT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NR_046268.1(TGFB2-AS1):n.290+91_290+94del variant causes a intron, non coding transcript 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
NR_046268.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

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 made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TGFB2-AS1	NR_046268.1 linkuse as main transcript	n.290+91_290+94del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TGFB2-AS1	ENST00000689961.2 linkuse as main transcript	n.697+42_697+45del		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome

AF:

1.00

Gnomad4 AMR exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.833

Gnomad4 NFE exome

AF:

0.750

GnomAD4 genome

AF:

0.862

AC:

130896

AN:

151866

Hom.:

56658

Cov.:

AF XY:

0.857

AC XY:

63602

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.944

Gnomad4 AMR

AF:

0.826

Gnomad4 ASJ

AF:

0.826

Gnomad4 EAS

AF:

0.796

Gnomad4 SAS

AF:

0.707

Gnomad4 FIN

AF:

0.829

Gnomad4 NFE

AF:

0.843

Gnomad4 OTH

AF:

0.847

Alfa

AF:

0.855

Hom.:

6778

Bravo

AF:

0.868

Asia WGS

AF:

0.757

AC:

2631

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over