chr12-114690850-A-T

Variant names:

• chr12-114690850-A-T
• rs1910047
• ENST00000653540.1:n.196+7714A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653540.1(TBX3-AS1):​n.196+7714A>T variant causes a intron 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 ENST00000653540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 3 publications found

Genes affected

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

ENSG00000309206 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TBX3-AS1	NR_187552.1	n.343+8216A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX3-AS1	ENST00000653540.1	n.196+7714A>T		intron_variant	Intron 1 of 3
TBX3-AS1	ENST00000660721.1	n.343+8216A>T		intron_variant	Intron 1 of 1
TBX3-AS1	ENST00000839282.1	n.288+8216A>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0765 AC: 3170 AN: 41464

American (AMR) AF: 0.388 AC: 5919 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1469 AN: 3470

East Asian (EAS) AF: 0.0962 AC: 497 AN: 5166

South Asian (SAS) AF: 0.237 AC: 1134 AN: 4790

European-Finnish (FIN) AF: 0.221 AC: 2333 AN: 10544

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19060 AN: 67932

Other (OTH) AF: 0.272 AC: 573 AN: 2108

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
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1910047; hg19: chr12-115128655;