17-61395042-G-A

Variant names:

• chr17-61395042-G-A
• rs11079429
• ENST00000585765.1:n.28+5174C>T

Variant summary

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

The ENST00000585765.1(TBX2-AS1):​n.28+5174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,074 control chromosomes in the GnomAD database, including 21,398 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 0.48 (21398 hom., cov: 33)
• Consequence: TBX2-AS1 ENST00000585765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585765.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBX2-AS1	NR_125749.1		n.571-1295C>T		intron	N/A
	TBX2-AS1	NR_125750.1		n.369-304C>T		intron	N/A
	TBX2-AS1	NR_125751.1		n.369-1295C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBX2-AS1	ENST00000585765.1	TSL:5	n.28+5174C>T		intron	N/A
	TBX2-AS1	ENST00000586706.6	TSL:3	n.332-304C>T		intron	N/A
	TBX2-AS1	ENST00000589814.6	TSL:3	n.342-304C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72935 AN: 151956 Hom.: 21398 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.512

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.480 AC: 72927 AN: 152074 Hom.: 21398 Cov.: 33 AF XY: 0.479 AC XY: 35567 AN XY: 74314

African (AFR) AF: 0.150 AC: 6215 AN: 41496

American (AMR) AF: 0.432 AC: 6612 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2190 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1496 AN: 5162

South Asian (SAS) AF: 0.476 AC: 2289 AN: 4810

European-Finnish (FIN) AF: 0.668 AC: 7058 AN: 10570

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45245 AN: 67954

Other (OTH) AF: 0.512 AC: 1083 AN: 2114

Alfa AF: 0.583 Hom.: 35742

Bravo AF: 0.447

Asia WGS AF: 0.363 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.43
PhyloP100		-0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Other links and lift over

dbSNP: rs11079429; hg19: chr17-59472403;