3-189006021-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.210
Variant links:
Genes affected
TPRG1 (HGNC:24759): (tumor protein p63 regulated 1) Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TPRG1XR_001740120.3 linkn.3903+1261G>C intron_variant Intron 2 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TPRG1ENST00000433971.5 linkc.-660+1261G>C intron_variant Intron 3 of 10 2 ENSP00000412547.1 Q6ZUI0
TPRG1ENST00000496671.1 linkn.473+1261G>C intron_variant Intron 3 of 3 4

Frequencies

GnomAD3 genomes
AF:
0.888
AC:
135015
AN:
152038
Hom.:
61825
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.636
Gnomad4 AMR
AF:
0.958
Gnomad4 ASJ
AF:
0.984
Gnomad4 EAS
AF:
0.910
Gnomad4 SAS
AF:
0.930
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.996
Gnomad4 OTH
AF:
0.927
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 v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.87
DANN
Benign
0.29

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs710507; hg19: chr3-188723810; API