rs10499902

Variant names:

• chr7-87335653-A-G
• rs10499902
• ENST00000359941.12:n.661-5559T>C

Variant summary

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

The ENST00000359941.12(TP53TG1):​n.661-5559T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,332 control chromosomes in the GnomAD database, including 466 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 0.051 (466 hom., cov: 33)
• Consequence: TP53TG1 ENST00000359941.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TP53TG1	NR_015381.1	n.612+5870T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TP53TG1	ENST00000359941.12	n.661-5559T>C		intron_variant	Intron 2 of 3	1
TP53TG1	ENST00000416560.8	n.637+5870T>C		intron_variant	Intron 3 of 3	1
TP53TG1	ENST00000421293.5	n.454+5870T>C		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7716 AN: 152214 Hom.: 466 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0507 AC: 7724 AN: 152332 Hom.: 466 Cov.: 33 AF XY: 0.0490 AC XY: 3654 AN XY: 74498

African (AFR) AF: 0.144 AC: 5986 AN: 41556

American (AMR) AF: 0.0255 AC: 390 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00374 AC: 13 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5194

South Asian (SAS) AF: 0.0244 AC: 118 AN: 4828

European-Finnish (FIN) AF: 0.0137 AC: 146 AN: 10622

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0140 AC: 955 AN: 68036

Other (OTH) AF: 0.0402 AC: 85 AN: 2116

Alfa AF: 0.0314 Hom.: 46

Bravo AF: 0.0555

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.55
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10499902; hg19: chr7-86964969;