rs2062713

chr12-114738747-C-T

Variant summary

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

The ENST00000660721.1(TBX3-AS1):n.344-28537C>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 0.394 in 151,990 control chromosomes in the GnomAD database, including 12,784 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 0.39 (12784 hom., cov: 32)
• Consequence: TBX3-AS1 ENST00000660721.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX3-AS1	XR_007063471.1	n.2039+3387C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX3-AS1	ENST00000660721.1	n.344-28537C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59837 AN: 151872 Hom.: 12780 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.394 AC: 59853 AN: 151990 Hom.: 12784 Cov.: 32 AF XY: 0.393 AC XY: 29204 AN XY: 74290

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.434

Alfa AF: 0.452 Hom.: 3962

Bravo AF: 0.397

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.82
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2062713; hg19: chr12-115176552;