17-61399149-G-C

Variant names:

• chr17-61399149-G-C
• rs4455026
• ENST00000590421.2:n.458C>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.458C>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 0.0873 in 152,320 control chromosomes in the GnomAD database, including 839 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 0.087 (839 hom., cov: 33)
  • Exomes 𝑓: 0.037 (0 hom.)
• Consequence: TBX2-AS1 ENST00000590421.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838
• 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 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.458C>G		non_coding_transcript_exon	Exon 1 of 2
	TBX2-AS1	NR_125750.1		n.368+90C>G		intron	N/A
	TBX2-AS1	NR_125751.1		n.368+90C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBX2-AS1	ENST00000590421.2	TSL:2	n.458C>G		non_coding_transcript_exon	Exon 1 of 2
	TBX2-AS1	ENST00000585765.1	TSL:5	n.28+1067C>G		intron	N/A
	TBX2-AS1	ENST00000586706.6	TSL:3	n.91+90C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13263 AN: 152120 Hom.: 831 Cov.: 33

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0873

GnomAD4 exome AF: 0.0366 AC: 3 AN: 82 Hom.: 0 Cov.: 0 AF XY: 0.0455 AC XY: 3 AN XY: 66

African (AFR) AF: 0.00 AC: 0 AN: 4

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: 0.0395 AC: 3 AN: 76

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0873 AC: 13296 AN: 152238 Hom.: 839 Cov.: 33 AF XY: 0.0927 AC XY: 6903 AN XY: 74440

African (AFR) AF: 0.0752 AC: 3123 AN: 41556

American (AMR) AF: 0.170 AC: 2605 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1503 AN: 5152

South Asian (SAS) AF: 0.126 AC: 608 AN: 4820

European-Finnish (FIN) AF: 0.110 AC: 1166 AN: 10616

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0572 AC: 3889 AN: 68012

Other (OTH) AF: 0.0864 AC: 182 AN: 2106

Alfa AF: 0.0687 Hom.: 54

Bravo AF: 0.0913

Asia WGS AF: 0.177 AC: 614 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.8
DANN	Benign	0.64
PhyloP100		0.84
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4455026;

hg19: chr17-59476510;