7-87330539-C-T

Position:

• chr7-87330539-C-T

Variant summary

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

The ENST00000359941.11(TP53TG1):​n.655-445G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0465 in 152,188 control chromosomes in the GnomAD database, including 213 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 0.046 (213 hom., cov: 32)
• Consequence: TP53TG1 ENST00000359941.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

TP53TG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TP53TG1	NR_015381.1	n.613-5095G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TP53TG1	ENST00000359941.11	n.655-445G>A		intron_variant		1
TP53TG1	ENST00000416560.7	n.590-5095G>A		intron_variant		1
TP53TG1	ENST00000421293.4	n.419-5095G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0465 AC: 7065 AN: 152070 Hom.: 213 Cov.: 32

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0224

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00414

Gnomad FIN AF: 0.0707

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0465 AC: 7073 AN: 152188 Hom.: 213 Cov.: 32 AF XY: 0.0460 AC XY: 3420 AN XY: 74388

Gnomad4 AFR AF: 0.0569

Gnomad4 AMR AF: 0.0224

Gnomad4 ASJ AF: 0.0438

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.0707

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0194 Hom.: 10

Bravo AF: 0.0438

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	7.7
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs802049; hg19: chr7-86959855;