ENST00000630391.1:n.596+13009C>T

Variant names:

• chr3-24602082-C-T
• rs12631757
• ENST00000630391.1:n.596+13009C>T

Variant summary

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

The ENST00000630391.1(THRB-AS1):​n.596+13009C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,028 control chromosomes in the GnomAD database, including 2,295 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 0.17 (2295 hom., cov: 32)
• Consequence: THRB-AS1 ENST00000630391.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

THRB-AS1 (HGNC:44515): (THRB antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THRB-AS1	ENST00000630391.1	n.596+13009C>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25784 AN: 151910 Hom.: 2296 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.170 AC: 25794 AN: 152028 Hom.: 2295 Cov.: 32 AF XY: 0.173 AC XY: 12825 AN XY: 74308

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.163

Alfa AF: 0.163 Hom.: 1541

Bravo AF: 0.168

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12631757; hg19: chr3-24643573;