12-114700839-G-A

Position:

• chr12-114700839-G-A

Variant summary

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

The ENST00000660721.1(TBX3-AS1):​n.343+18205G>A 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 0.897 in 152,180 control chromosomes in the GnomAD database, including 61,475 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 0.90 (61475 hom., cov: 32)
• Consequence: TBX3-AS1 ENST00000660721.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 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+18205G>A		intron_variant, non_coding_transcript_variant
TBX3-AS1	ENST00000653540.1	n.196+17703G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136367 AN: 152062 Hom.: 61414 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.897 AC: 136489 AN: 152180 Hom.: 61475 Cov.: 32 AF XY: 0.892 AC XY: 66365 AN XY: 74382

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.915

Alfa AF: 0.889 Hom.: 87236

Bravo AF: 0.903

Asia WGS AF: 0.822 AC: 2858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.72
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6489968; hg19: chr12-115138644;