ENST00000589814.6:n.49G>A

Variant names:

• chr17-61399531-C-T
• rs2286524
• ENST00000589814.6:n.49G>A

Variant summary

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

The ENST00000589814.6(TBX2-AS1):​n.49G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0926 in 152,298 control chromosomes in the GnomAD database, including 906 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 0.093 (906 hom., cov: 33)
  • Exomes 𝑓: 0.048 (0 hom.)
• Consequence: TBX2-AS1 ENST00000589814.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 publications found

Genes affected

TBX2-AS1 (HGNC:50355): (TBX2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBX2-AS1	NR_125749.1	n.76G>A		non_coding_transcript_exon_variant	Exon 1 of 2
TBX2-AS1	NR_125750.1	n.76G>A		non_coding_transcript_exon_variant	Exon 1 of 3
TBX2-AS1	NR_125751.1	n.76G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX2-AS1	ENST00000589814.6	n.49G>A		non_coding_transcript_exon_variant	Exon 1 of 3	3
TBX2-AS1	ENST00000590421.2	n.76G>A		non_coding_transcript_exon_variant	Exon 1 of 2	2
TBX2-AS1	ENST00000591313.8	n.79G>A		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14053 AN: 152066 Hom.: 897 Cov.: 33

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.0898

GnomAD4 exome AF: 0.0484 AC: 6 AN: 124 Hom.: 0 Cov.: 0 AF XY: 0.0510 AC XY: 5 AN XY: 98

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0431 AC: 5 AN: 116

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0926 AC: 14092 AN: 152174 Hom.: 906 Cov.: 33 AF XY: 0.0979 AC XY: 7284 AN XY: 74386

African (AFR) AF: 0.0948 AC: 3937 AN: 41538

American (AMR) AF: 0.173 AC: 2639 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3470

East Asian (EAS) AF: 0.290 AC: 1485 AN: 5124

South Asian (SAS) AF: 0.125 AC: 603 AN: 4834

European-Finnish (FIN) AF: 0.109 AC: 1161 AN: 10604

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0567 AC: 3857 AN: 67992

Other (OTH) AF: 0.0888 AC: 188 AN: 2116

Alfa AF: 0.0721 Hom.: 62

Bravo AF: 0.0978

Asia WGS AF: 0.178 AC: 616 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	13
DANN	Benign	0.96
PhyloP100		-1.2
PromoterAI		-0.0062	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8

Splicing

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

Other links and lift over

dbSNP: rs2286524; hg19: chr17-59476892; COSMIC: COSV107270566;