rs710506

Variant names:

• chr3-189005288-A-G
• rs710506
• ENST00000433971.5:c.-660+528A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-189005288-A-G
• chr3-189005288-A-T

Variant summary

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

The ENST00000433971.5(TPRG1):​c.-660+528A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,130 control chromosomes in the GnomAD database, including 61,841 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 0.89 (61841 hom., cov: 33)
• Consequence: TPRG1 ENST00000433971.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733
• Publications: 2 publications found

Genes affected

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

ENSG00000305951 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433971.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPRG1	ENST00000433971.5	TSL:2	c.-660+528A>G		intron	N/A	ENSP00000412547.1	Q6ZUI0
	TPRG1	ENST00000867713.1		c.-571+528A>G		intron	N/A	ENSP00000537772.1
	TPRG1	ENST00000867714.1		c.-1380+528A>G		intron	N/A	ENSP00000537773.1

Frequencies

GnomAD3 genomes AF: 0.888 AC: 134999 AN: 152012 Hom.: 61822 Cov.: 33

Gnomad AFR AF: 0.636

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.930

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.888 AC: 135066 AN: 152130 Hom.: 61841 Cov.: 33 AF XY: 0.891 AC XY: 66243 AN XY: 74378

African (AFR) AF: 0.636 AC: 26360 AN: 41464

American (AMR) AF: 0.958 AC: 14616 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3415 AN: 3472

East Asian (EAS) AF: 0.909 AC: 4689 AN: 5156

South Asian (SAS) AF: 0.930 AC: 4491 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10625 AN: 10626

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67713 AN: 68006

Other (OTH) AF: 0.928 AC: 1961 AN: 2114

Alfa AF: 0.951 Hom.: 31938

Bravo AF: 0.875

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.64
PhyloP100		0.73
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs710506;

hg19: chr3-188723077;