3-189265019-G-A

Position:

• chr3-189265019-G-A

Variant summary

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

The NM_198485.4(TPRG1):​c.479+26110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,012 control chromosomes in the GnomAD database, including 25,168 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 0.56 (25168 hom., cov: 32)
• Consequence: TPRG1 NM_198485.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPRG1	NM_198485.4	c.479+26110G>A		intron_variant		ENST00000345063.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPRG1	ENST00000345063.8	c.479+26110G>A		intron_variant		1	NM_198485.4	P1
TPRG1	ENST00000425670.1	c.261+26110G>A		intron_variant		3
TPRG1	ENST00000433971.5	c.479+26110G>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85004 AN: 151894 Hom.: 25121 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.560 AC: 85107 AN: 152012 Hom.: 25168 Cov.: 32 AF XY: 0.555 AC XY: 41196 AN XY: 74272

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.538

Alfa AF: 0.523 Hom.: 12314

Bravo AF: 0.555

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.20

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: rs1000291; hg19: chr3-188982808;