rs802032

Variant names:

• chr7-87333934-G-A
• rs802032
• ENST00000359941.12:n.661-3840C>T

Variant summary

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

The ENST00000359941.12(TP53TG1):​n.661-3840C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,154 control chromosomes in the GnomAD database, including 1,687 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 0.11 (1687 hom., cov: 32)
• Consequence: TP53TG1 ENST00000359941.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TP53TG1	NR_015381.1	n.612+7589C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TP53TG1	ENST00000359941.12	n.661-3840C>T		intron_variant	Intron 2 of 3	1
TP53TG1	ENST00000416560.8	n.637+7589C>T		intron_variant	Intron 3 of 3	1
TP53TG1	ENST00000421293.5	n.454+7589C>T		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17270 AN: 152036 Hom.: 1671 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.0541

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.114 AC: 17328 AN: 152154 Hom.: 1687 Cov.: 32 AF XY: 0.113 AC XY: 8423 AN XY: 74356

African (AFR) AF: 0.266 AC: 11036 AN: 41462

American (AMR) AF: 0.0871 AC: 1332 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0541 AC: 188 AN: 3472

East Asian (EAS) AF: 0.00676 AC: 35 AN: 5180

South Asian (SAS) AF: 0.0648 AC: 313 AN: 4830

European-Finnish (FIN) AF: 0.0702 AC: 743 AN: 10582

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0503 AC: 3424 AN: 68018

Other (OTH) AF: 0.0923 AC: 195 AN: 2112

Alfa AF: 0.0605 Hom.: 494

Bravo AF: 0.119

Asia WGS AF: 0.0500 AC: 173 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	2.4
DANN	Benign	0.55
PhyloP100		0.64
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: rs802032; hg19: chr7-86963250;