dbSNP rs10131293: TRA:n.22461166G>A (chr14-22461166-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.147 in 149,806 control chromosomes in the GnomAD database, including 2,753 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 0.15 ( 2753 hom., cov: 23)

Consequence

TRA
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

Publications

2 publications found

Variant links:

Genes affected

TRA (HGNC:12027):

TRA links:

TRD (HGNC:12252):

TRD links:

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

TRD-AS1 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TRA		n.22461166G>A	intragenic_variant
TRD		n.22461166G>A	intragenic_variant
TRD-AS1	NR_148361.1 link	n.225+20075C>T	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000514473.2 link	n.225+20075C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22043

AN:

149688

Hom.:

2747

Cov.:

show subpopulations

Gnomad AFR

AF:

0.346

Gnomad AMI

AF:

0.0521

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.0989

Gnomad EAS

AF:

0.000583

Gnomad SAS

AF:

0.0269

Gnomad FIN

AF:

0.0629

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0750

Gnomad OTH

AF:

0.139

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

GnomAD4 genome

AF:

0.147

AC:

22071

AN:

149806

Hom.:

2753

Cov.:

AF XY:

0.144

AC XY:

10536

AN XY:

73222

show subpopulations

African (AFR)

AF:

0.345

AC:

13952

AN:

40392

American (AMR)

AF:

0.105

AC:

1574

AN:

14944

Ashkenazi Jewish (ASJ)

AF:

0.0989

AC:

341

AN:

3448

East Asian (EAS)

AF:

0.000584

AC:

AN:

5138

South Asian (SAS)

AF:

0.0263

AC:

124

AN:

4722

European-Finnish (FIN)

AF:

0.0629

AC:

649

AN:

10312

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0750

AC:

5068

AN:

67570

Other (OTH)

AF:

0.138

AC:

287

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

784

1569

2353

3138

3922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0613

Hom.:

160

Bravo

AF:

0.161

Asia WGS

AF:

0.0360

AC:

128

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

(source)

DANN

Benign

0.71

PhyloP100

-1.5

Splicing

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

Publications

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rs10131293

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