chr17-61399054-T-C

Variant names:

• chr17-61399054-T-C
• rs1476781
• ENST00000590421.2:n.553A>G

Variant summary

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

The ENST00000590421.2(TBX2-AS1):​n.553A>G 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 0.771 in 152,158 control chromosomes in the GnomAD database, including 45,450 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 0.77 (45444 hom., cov: 34)
  • Exomes 𝑓: 0.73 (6 hom.)
• Consequence: TBX2-AS1 ENST00000590421.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 8 publications found

Genes affected

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

ENSG00000289926 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590421.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBX2-AS1	NR_125749.1		n.553A>G		non_coding_transcript_exon	Exon 1 of 2
	TBX2-AS1	NR_125750.1		n.368+185A>G		intron	N/A
	TBX2-AS1	NR_125751.1		n.368+185A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBX2-AS1	ENST00000590421.2	TSL:2	n.553A>G		non_coding_transcript_exon	Exon 1 of 2
	TBX2-AS1	ENST00000722645.1		n.401A>G		non_coding_transcript_exon	Exon 2 of 3
	TBX2-AS1	ENST00000722655.1		n.87A>G		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117256 AN: 152022 Hom.: 45397 Cov.: 34

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.755

GnomAD4 exome AF: 0.727 AC: 16 AN: 22 Hom.: 6 Cov.: 0 AF XY: 0.643 AC XY: 9 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 16 AN: 20

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.771 AC: 117362 AN: 152136 Hom.: 45444 Cov.: 34 AF XY: 0.771 AC XY: 57311 AN XY: 74370

African (AFR) AF: 0.787 AC: 32668 AN: 41528

American (AMR) AF: 0.704 AC: 10765 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2595 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3542 AN: 5124

South Asian (SAS) AF: 0.665 AC: 3207 AN: 4820

European-Finnish (FIN) AF: 0.835 AC: 8844 AN: 10588

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53196 AN: 67984

Other (OTH) AF: 0.752 AC: 1589 AN: 2112

Alfa AF: 0.782 Hom.: 6003

Bravo AF: 0.763

Asia WGS AF: 0.680 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.43
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs1476781; hg19: chr17-59476415;