rs802032

chr7-87333934-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_015381.1(TP53TG1):n.612+7589C>T variant causes a intron, non coding transcript 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 NR_015381.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TP53TG1	NR_015381.1	n.612+7589C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TP53TG1	ENST00000661943.3	n.671+7589C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.0541

Gnomad4 EAS AF: 0.00676

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0503

Gnomad4 OTH AF: 0.0923

Alfa AF: 0.0804 Hom.: 106

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs802032; hg19: chr7-86963250;