chr7-87330539-C-T

Variant names:

• chr7-87330539-C-T
• rs802049
• ENST00000359941.12:n.661-445G>A

Variant summary

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

The ENST00000359941.12(TP53TG1):​n.661-445G>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 ENST00000359941.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• 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=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000359941.12. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TP53TG1	NR_015381.1		n.613-5095G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TP53TG1	ENST00000359941.12	TSL:1	n.661-445G>A		intron	N/A
	TP53TG1	ENST00000416560.8	TSL:1	n.638-5095G>A		intron	N/A
	TP53TG1	ENST00000421293.5	TSL:1	n.455-5095G>A		intron	N/A

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

African (AFR) AF: 0.0569 AC: 2364 AN: 41536

American (AMR) AF: 0.0224 AC: 342 AN: 15294

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

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5166

South Asian (SAS) AF: 0.00394 AC: 19 AN: 4826

European-Finnish (FIN) AF: 0.0707 AC: 748 AN: 10586

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0487 AC: 3309 AN: 67990

Other (OTH) AF: 0.0397 AC: 84 AN: 2116

Alfa AF: 0.0220 Hom.: 13

Bravo AF: 0.0438

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	7.7
DANN	Benign	0.93
PhyloP100		0.21
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: rs802049; hg19: chr7-86959855;