7-87331144-C-T

Position:

• chr7-87331144-C-T

Variant summary

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

The NR_015381.1(TP53TG1):​n.613-5700G>A 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 0.0451 in 152,110 control chromosomes in the GnomAD database, including 204 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 0.045 (204 hom., cov: 31)
• Consequence: TP53TG1 NR_015381.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TP53TG1	NR_015381.1	n.613-5700G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TP53TG1	ENST00000661943.3	n.672-5700G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6851 AN: 151992 Hom.: 204 Cov.: 31

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0222

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0451 AC: 6858 AN: 152110 Hom.: 204 Cov.: 31 AF XY: 0.0446 AC XY: 3316 AN XY: 74344

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.0222

Gnomad4 ASJ AF: 0.0438

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.00416

Gnomad4 FIN AF: 0.0706

Gnomad4 NFE AF: 0.0486

Gnomad4 OTH AF: 0.0384

Alfa AF: 0.0406 Hom.: 13

Bravo AF: 0.0421

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs802051; hg19: chr7-86960460;