rs802051

Variant names:

• chr7-87331144-C-T
• rs802051
• ENST00000359941.12:n.661-1050G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000359941.12(TP53TG1):​n.661-1050G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 152,110 control chromosomes in the GnomAD database, including 204 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 0.045 (204 hom., cov: 31)
• Consequence: TP53TG1 ENST00000359941.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TP53TG1	NR_015381.1	n.613-5700G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TP53TG1	ENST00000359941.12	n.661-1050G>A		intron_variant	Intron 2 of 3	1
TP53TG1	ENST00000416560.8	n.638-5700G>A		intron_variant	Intron 3 of 3	1
TP53TG1	ENST00000421293.5	n.455-5700G>A		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6851 AN: 151992 Hom.: 204 Cov.: 31

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0222

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0451 AC: 6858 AN: 152110 Hom.: 204 Cov.: 31 AF XY: 0.0446 AC XY: 3316 AN XY: 74344

African (AFR) AF: 0.0520 AC: 2157 AN: 41502

American (AMR) AF: 0.0222 AC: 339 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0438 AC: 152 AN: 3468

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5168

South Asian (SAS) AF: 0.00416 AC: 20 AN: 4810

European-Finnish (FIN) AF: 0.0706 AC: 746 AN: 10568

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0486 AC: 3306 AN: 67982

Other (OTH) AF: 0.0384 AC: 81 AN: 2110

Alfa AF: 0.0406 Hom.: 13

Bravo AF: 0.0421

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.53
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs802051; hg19: chr7-86960460;