Genetic Variant TRG-TCC2-1:c.-12C>T (chr1-146037049-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 ENST00000000000(TRG-TCC2-1):c.-12C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,086 control chromosomes in the GnomAD database, including 7,768 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 0.30 ( 7768 hom., cov: 32)

Consequence

TRG-TCC2-1
ENST00000000000 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -12.3

Publications

11 publications found

Variant links:

Genes affected

TRG-TCC2-1 (HGNC:34623):

TRG-TCC2-1 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=-0.47).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRG-TCC2-1	unassigned_transcript_156	c.-12C>T		upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.298

AC:

45293

AN:

151968

Hom.:

7769

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.463

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.329

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

GnomAD4 genome

AF:

0.298

AC:

45304

AN:

152086

Hom.:

7768

Cov.:

AF XY:

0.296

AC XY:

21977

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.140

AC:

5819

AN:

41498

American (AMR)

AF:

0.347

AC:

5292

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.308

AC:

1066

AN:

3464

East Asian (EAS)

AF:

0.169

AC:

876

AN:

5192

South Asian (SAS)

AF:

0.244

AC:

1177

AN:

4822

European-Finnish (FIN)

AF:

0.390

AC:

4123

AN:

10568

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.379

AC:

25774

AN:

67970

Other (OTH)

AF:

0.326

AC:

685

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1551

3101

4652

6202

7753

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.326

Hom.:

6305

Bravo

AF:

0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

0.0010

(source)

PhyloP100

-12

PromoterAI

-0.043

Neutral

(source)

Splicing

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

Publications

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1-146037049-C-T

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