rs73991913

chr17-61398955-C-Achr17-61398955-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_125751.1(TBX2-AS1):n.368+284G>T 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 0.0774 in 152,252 control chromosomes in the GnomAD database, including 1,470 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 0.077 (1470 hom., cov: 33)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: TBX2-AS1 NR_125751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.995

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX2-AS1	NR_125751.1	n.368+284G>T		intron_variant, non_coding_transcript_variant
TBX2-AS1	NR_125749.1	n.570+82G>T		intron_variant, non_coding_transcript_variant
TBX2-AS1	NR_125750.1	n.368+284G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000585765.1	n.28+1261G>T		intron_variant, non_coding_transcript_variant		5
TBX2-AS1	ENST00000592009.1	n.41-5208G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11748 AN: 152122 Hom.: 1464 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0334

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00123

Gnomad OTH AF: 0.0468

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0774 AC: 11788 AN: 152240 Hom.: 1470 Cov.: 33 AF XY: 0.0742 AC XY: 5524 AN XY: 74458

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.0334

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.0456

Gnomad4 SAS AF: 0.0101

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00123

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.00138 Hom.: 2

Bravo AF: 0.0883

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
Cadd	Benign	22
Dann	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73991913; hg19: chr17-59476316;