rs802047

chr7-87328469-T-C

Variant summary

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

The NR_015381.1(TP53TG1):n.613-3025A>G 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 0.277 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 NR_015381.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

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=-0.95).
• 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/exons	MANE	UniProt
TP53TG1	NR_015381.1	n.613-3025A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TP53TG1	ENST00000661943.3	n.672-3025A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42113 AN: 152094 Hom.: 9948 Cov.: 32

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.: 32 AF XY: 0.272 AC XY: 20275 AN XY: 74434

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0450

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.238

Alfa AF: 0.178 Hom.: 1598

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
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs802047; hg19: chr7-86957785;