17-61399149-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.368+90C>G 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 0.0873 in 152,320 control chromosomes in the GnomAD database, including 839 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 0.087 (839 hom., cov: 33)
  • Exomes 𝑓: 0.037 (0 hom.)
• Consequence: TBX2-AS1 NR_125751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838

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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX2-AS1	NR_125751.1	n.368+90C>G		intron_variant, non_coding_transcript_variant
TBX2-AS1	NR_125749.1	n.458C>G		non_coding_transcript_exon_variant	1/2
TBX2-AS1	NR_125750.1	n.368+90C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000585765.1	n.28+1067C>G		intron_variant, non_coding_transcript_variant		5
TBX2-AS1	ENST00000592009.1	n.41-5402C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13263 AN: 152120 Hom.: 831 Cov.: 33

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0873

GnomAD4 exome AF: 0.0366 AC: 3 AN: 82 Hom.: 0 Cov.: 0 AF XY: 0.0455 AC XY: 3 AN XY: 66

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.0395

GnomAD4 genome AF: 0.0873 AC: 13296 AN: 152238 Hom.: 839 Cov.: 33 AF XY: 0.0927 AC XY: 6903 AN XY: 74440

Gnomad4 AFR AF: 0.0752

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0572

Gnomad4 OTH AF: 0.0864

Alfa AF: 0.0687 Hom.: 54

Bravo AF: 0.0913

Asia WGS AF: 0.177 AC: 614 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	7.8
Dann	Benign	0.64
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.8

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4455026; hg19: chr17-59476510;