Genetic Variant TRB:n.142307399_142307400delTG (chr7-142307367-AGT-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.014 ( 18 hom., cov: 0)

Consequence

TRB
intragenic

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

1 publications found

Variant links:

Genes affected

TRB (HGNC:12155):

TRB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0141 (2062/146288) while in subpopulation NFE AF = 0.0171 (1136/66364). AF 95% confidence interval is 0.0163. There are 18 homozygotes in GnomAd4. There are 1026 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 18 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRB		n.142307399_142307400delTG		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0140

AC:

2051

AN:

146182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00627

Gnomad ASJ

AF:

0.00204

Gnomad EAS

AF:

0.00570

Gnomad SAS

AF:

0.0111

Gnomad FIN

AF:

0.0236

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0171

Gnomad OTH

AF:

0.0101

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

GnomAD4 genome

AF:

0.0141

AC:

2062

AN:

146288

Hom.:

Cov.:

AF XY:

0.0144

AC XY:

1026

AN XY:

71036

show subpopulations

African (AFR)

AF:

0.0127

AC:

502

AN:

39680

American (AMR)

AF:

0.00626

AC:

AN:

14692

Ashkenazi Jewish (ASJ)

AF:

0.00204

AC:

AN:

3424

East Asian (EAS)

AF:

0.00551

AC:

AN:

4900

South Asian (SAS)

AF:

0.0116

AC:

AN:

4486

European-Finnish (FIN)

AF:

0.0236

AC:

225

AN:

9544

Middle Eastern (MID)

AF:

0.00

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.0171

AC:

1136

AN:

66364

Other (OTH)

AF:

0.0105

AC:

AN:

2008

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

190

284

379

474

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0127

Hom.:

1268

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.6

Splicing

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

Publications

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7-142307367-AGT-A

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