dbSNP rs73991913: ENSG00000267131:n.28+1261G>T (chr17-61398955-C-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000590421.2(TBX2-AS1):n.570+82G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 152,252 control chromosomes in the GnomAD database, including 1,470 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 0.077 ( 1470 hom., cov: 33)

Exomes 𝑓: 0.083 ( 0 hom. )

Consequence

TBX2-AS1
ENST00000590421.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.995

Variant links:

Genes affected

ENSG00000267131 (HGNC:):

ENSG00000267131 links:

TBX2-AS1 (HGNC:50355): (TBX2 antisense RNA 1)

TBX2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TBX2-AS1	NR_125749.1 link	n.570+82G>T	intron_variant	Intron 1 of 1
TBX2-AS1	NR_125750.1 link	n.368+284G>T	intron_variant	Intron 1 of 2
TBX2-AS1	NR_125751.1 link	n.368+284G>T	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000267131	ENST00000585765.1 link	n.28+1261G>T	intron_variant	Intron 1 of 3	5
TBX2-AS1	ENST00000589814.5 link	n.132+284G>T	intron_variant	Intron 1 of 2	3
TBX2-AS1	ENST00000590421.2 link	n.570+82G>T	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.0772

AC:

11748

AN:

152122

Hom.:

1464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0334

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.0459

Gnomad SAS

AF:

0.0106

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00123

Gnomad OTH

AF:

0.0468

GnomAD4 exome

AF:

0.0833

AC:

AN:

Hom.:

AF XY:

0.100

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0774

AC:

11788

AN:

152240

Hom.:

1470

Cov.:

AF XY:

0.0742

AC XY:

5524

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.260

Gnomad4 AMR

AF:

0.0334

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.0456

Gnomad4 SAS

AF:

0.0101

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00123

Gnomad4 OTH

AF:

0.0464

Alfa

AF:

0.00138

Hom.:

Bravo

AF:

0.0883

Asia WGS

AF:

0.0600

AC:

208

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Benign

0.95

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over