17-61399054-T-C

Position:

• chr17-61399054-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125751.1(TBX2-AS1):​n.368+185A>G variant causes a intron, non coding transcript 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 NR_125751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBX2-AS1	NR_125751.1	n.368+185A>G		intron_variant, non_coding_transcript_variant
TBX2-AS1	NR_125749.1	n.553A>G		non_coding_transcript_exon_variant	1/2
TBX2-AS1	NR_125750.1	n.368+185A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000585765.1	n.28+1162A>G		intron_variant, non_coding_transcript_variant		5
TBX2-AS1	ENST00000592009.1	n.41-5307A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.800

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

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.752

Alfa AF: 0.785 Hom.: 5814

Bravo AF: 0.763

Asia WGS AF: 0.680 AC: 2366 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	8.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476781; hg19: chr17-59476415;