rs1450118

Positions:

• chr3-189218969-A-G

Variant summary

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

The NM_198485.4(TPRG1):​c.302+3586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,950 control chromosomes in the GnomAD database, including 21,923 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 0.54 (21923 hom., cov: 31)
• Consequence: TPRG1 NM_198485.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

Genes affected

TPRG1 (HGNC:24759): (tumor protein p63 regulated 1) Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPRG1	NM_198485.4	c.302+3586A>G		intron_variant		ENST00000345063.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPRG1	ENST00000345063.8	c.302+3586A>G		intron_variant		1	NM_198485.4	P1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81451 AN: 151832 Hom.: 21898 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.536 AC: 81517 AN: 151950 Hom.: 21923 Cov.: 31 AF XY: 0.534 AC XY: 39644 AN XY: 74250

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.573

Alfa AF: 0.549 Hom.: 16230

Bravo AF: 0.533

Asia WGS AF: 0.615 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1450118; hg19: chr3-188936758;