3-189006021-G-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.86).
• 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
TPRG1	XR_001740120.3	n.3903+1261G>C		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPRG1	ENST00000433971.5	c.-660+1261G>C		intron_variant	Intron 3 of 10	2		ENSP00000412547.1
TPRG1	ENST00000496671.1	n.473+1261G>C		intron_variant	Intron 3 of 3	4

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

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

Other links and lift over

dbSNP: rs710507; hg19: chr3-188723810;