rs73991913

Variant names:

• chr17-61398955-C-A
• rs73991913
• ENST00000585765.1:n.28+1261G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-61398955-C-A
• chr17-61398955-C-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000585765.1(TBX2-AS1):​n.28+1261G>T variant causes a intron 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 ENST00000585765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.995
• Publications: 1 publications found

Genes affected

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

ENSG00000289926 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TBX2-AS1	NR_125749.1	n.570+82G>T		intron_variant	Intron 1 of 1
TBX2-AS1	NR_125750.1	n.368+284G>T		intron_variant	Intron 1 of 2
TBX2-AS1	NR_125751.1	n.368+284G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX2-AS1	ENST00000585765.1	n.28+1261G>T		intron_variant	Intron 1 of 3	5
TBX2-AS1	ENST00000586706.6	n.91+284G>T		intron_variant	Intron 1 of 3	3
TBX2-AS1	ENST00000589814.6	n.341+284G>T		intron_variant	Intron 1 of 2	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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.260 AC: 10798 AN: 41498

American (AMR) AF: 0.0334 AC: 511 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.0456 AC: 236 AN: 5170

South Asian (SAS) AF: 0.0101 AC: 49 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00123 AC: 84 AN: 68032

Other (OTH) AF: 0.0464 AC: 98 AN: 2114

Alfa AF: 0.0133 Hom.: 23

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
PhyloP100		0.99
Mutation Taster		=96/4	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs73991913; hg19: chr17-59476316;