chr12-114738747-C-T

Variant names:

• chr12-114738747-C-T
• rs2062713
• ENST00000551875.1:n.542-9349C>T

Variant summary

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

The ENST00000551875.1(TBX3-AS1):​n.542-9349C>T variant causes a intron 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 ENST00000551875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TBX3-AS1	NR_187552.1	n.344-28537C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX3-AS1	ENST00000551875.1	n.542-9349C>T		intron_variant	Intron 3 of 4	2
TBX3-AS1	ENST00000653540.1	n.197-9349C>T		intron_variant	Intron 1 of 3
TBX3-AS1	ENST00000660721.1	n.344-28537C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.231 AC: 9573 AN: 41456

American (AMR) AF: 0.498 AC: 7601 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1355 AN: 5150

South Asian (SAS) AF: 0.308 AC: 1482 AN: 4818

European-Finnish (FIN) AF: 0.450 AC: 4752 AN: 10552

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31613 AN: 67956

Other (OTH) AF: 0.434 AC: 915 AN: 2110

Alfa AF: 0.448 Hom.: 3985

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2062713; hg19: chr12-115176552;