3-189006021-G-C

Variant names:

• chr3-189006021-G-C
• rs710507
• ENST00000433971.5:c.-660+1261G>C

Variant summary

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

The ENST00000433971.5(TPRG1):​c.-660+1261G>C 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 152,156 control chromosomes in the GnomAD database, including 61,844 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 (61844 hom., cov: 32)
• Consequence: TPRG1 ENST00000433971.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 0 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=-0.86).
• 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+1261G>C		intron	N/A	ENSP00000412547.1	Q6ZUI0
	TPRG1	ENST00000867713.1		c.-571+1261G>C		intron	N/A	ENSP00000537772.1
	TPRG1	ENST00000867714.1		c.-1380+1261G>C		intron	N/A	ENSP00000537773.1

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135015 AN: 152038 Hom.: 61825 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.930

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.888 AC: 135082 AN: 152156 Hom.: 61844 Cov.: 32 AF XY: 0.890 AC XY: 66271 AN XY: 74420

African (AFR) AF: 0.636 AC: 26359 AN: 41464

American (AMR) AF: 0.958 AC: 14636 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3413 AN: 3470

East Asian (EAS) AF: 0.910 AC: 4703 AN: 5170

South Asian (SAS) AF: 0.930 AC: 4485 AN: 4820

European-Finnish (FIN) AF: 1.00 AC: 10621 AN: 10622

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

European-Non Finnish (NFE) AF: 0.996 AC: 67711 AN: 68010

Other (OTH) AF: 0.927 AC: 1958 AN: 2112

Alfa AF: 0.936 Hom.: 3409

Bravo AF: 0.874

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	-0.86
CADD	Benign	0.87
DANN	Benign	0.29
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs710507;

hg19: chr3-188723810;