dbSNP rs802047: TP53TG1:n.820+1466A>G (chr7-87328469-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000359941.12(TP53TG1):n.820+1466A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,212 control chromosomes in the GnomAD database, including 9,993 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 0.28 ( 9993 hom., cov: 32)

Consequence

TP53TG1
ENST00000359941.12 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.928

Publications

2 publications found

Variant links:

Genes affected

TP53TG1 (HGNC:17026): (TP53 target 1)

TP53TG1 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TP53TG1	NR_015381.1 link	n.613-3025A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TP53TG1	ENST00000359941.12 link	n.820+1466A>G	intron_variant	Intron 3 of 3	1
TP53TG1	ENST00000416560.8 link	n.638-3025A>G	intron_variant	Intron 3 of 3	1
TP53TG1	ENST00000421293.5 link	n.455-3025A>G	intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42113

AN:

152094

Hom.:

9948

Cov.:

show subpopulations

Gnomad AFR

AF:

0.649

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.0451

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.237

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

GnomAD4 genome

AF:

0.277

AC:

42220

AN:

152212

Hom.:

9993

Cov.:

AF XY:

0.272

AC XY:

20275

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.650

AC:

26964

AN:

41496

American (AMR)

AF:

0.208

AC:

3181

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

480

AN:

3470

East Asian (EAS)

AF:

0.0450

AC:

233

AN:

5176

South Asian (SAS)

AF:

0.154

AC:

742

AN:

4832

European-Finnish (FIN)

AF:

0.123

AC:

1310

AN:

10616

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.126

AC:

8599

AN:

68008

Other (OTH)

AF:

0.238

AC:

504

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1188

2376

3565

4753

5941

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.184

Hom.:

1955

Bravo

AF:

0.299

Asia WGS

AF:

0.126

AC:

437

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

4.7

(source)

DANN

Benign

0.43

PhyloP100

-0.93

Mutation Taster

=100/0

polymorphism (auto)

(source)

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