dbSNP rs12631757: THRB-AS1:n.596+13009C>T (chr3-24602082-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0530

Publications

3 publications found

Variant links:

Genes affected

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

THRB-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 link	n.596+13009C>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25784

AN:

151910

Hom.:

2296

Cov.:

show subpopulations

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.:

AF XY:

0.173

AC XY:

12825

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.162

AC:

6718

AN:

41488

American (AMR)

AF:

0.203

AC:

3093

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

761

AN:

3468

East Asian (EAS)

AF:

0.163

AC:

837

AN:

5142

South Asian (SAS)

AF:

0.185

AC:

893

AN:

4822

European-Finnish (FIN)

AF:

0.210

AC:

2216

AN:

10564

Middle Eastern (MID)

AF:

0.193

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.159

AC:

10801

AN:

67966

Other (OTH)

AF:

0.163

AC:

343

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1086

2172

3258

4344

5430

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.163

Hom.:

4567

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

(source)

DANN

Benign

0.75

PhyloP100

-0.053

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over