rs11079429

chr17-61395042-G-Achr17-61395042-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125751.1(TBX2-AS1):n.369-1295C>T 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 0.48 in 152,074 control chromosomes in the GnomAD database, including 21,398 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 0.48 (21398 hom., cov: 33)
• Consequence: TBX2-AS1 NR_125751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX2-AS1	NR_125751.1	n.369-1295C>T		intron_variant, non_coding_transcript_variant
TBX2-AS1	NR_125749.1	n.571-1295C>T		intron_variant, non_coding_transcript_variant
TBX2-AS1	NR_125750.1	n.369-304C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000585765.1	n.28+5174C>T		intron_variant, non_coding_transcript_variant		5
TBX2-AS1	ENST00000592009.1	n.41-1295C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72935 AN: 151956 Hom.: 21398 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.512

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.480 AC: 72927 AN: 152074 Hom.: 21398 Cov.: 33 AF XY: 0.479 AC XY: 35567 AN XY: 74314

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.512

Alfa AF: 0.602 Hom.: 28567

Bravo AF: 0.447

Asia WGS AF: 0.363 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.0
Dann	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11079429; hg19: chr17-59472403;