rs1910047

chr12-114690850-A-T

Variant summary

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

The ENST00000660721.1(TBX3-AS1):n.343+8216A>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 0.227 in 151,936 control chromosomes in the GnomAD database, including 4,917 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 0.23 (4917 hom., cov: 31)
• Consequence: TBX3-AS1 ENST00000660721.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

Genes affected

TBX3-AS1 (HGNC:55471): (TBX3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX3-AS1	ENST00000660721.1	n.343+8216A>T		intron_variant, non_coding_transcript_variant
TBX3-AS1	ENST00000653540.1	n.196+7714A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34446 AN: 151818 Hom.: 4915 Cov.: 31

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.227 AC: 34458 AN: 151936 Hom.: 4917 Cov.: 31 AF XY: 0.227 AC XY: 16873 AN XY: 74260

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.0962

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.272

Alfa AF: 0.244 Hom.: 713

Bravo AF: 0.233

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.1
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1910047; hg19: chr12-115128655;