3-188976743-G-T

Variant names:

• chr3-188976743-G-T
• rs710492
• ENST00000433971.5:c.-1015-24031G>T

Variant summary

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

The ENST00000433971.5(TPRG1):​c.-1015-24031G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.969 in 152,348 control chromosomes in the GnomAD database, including 71,676 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 0.97 (71655 hom., cov: 32)
  • Exomes 𝑓: 1.0 (21 hom.)
• Consequence: TPRG1 ENST00000433971.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPRG1	ENST00000433971.5	c.-1015-24031G>T		intron_variant	Intron 1 of 10	2		ENSP00000412547.1
TPRG1	ENST00000496671.1	n.-11G>T		upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.969 AC: 147544 AN: 152188 Hom.: 71618 Cov.: 32

Gnomad AFR AF: 0.918

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.939

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.978

GnomAD4 exome AF: 1.00 AC: 42 AN: 42 Hom.: 21 Cov.: 0 AF XY: 1.00 AC XY: 36 AN XY: 36

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 34 AN: 34

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.969 AC: 147634 AN: 152306 Hom.: 71655 Cov.: 32 AF XY: 0.969 AC XY: 72127 AN XY: 74466

African (AFR) AF: 0.917 AC: 38124 AN: 41554

American (AMR) AF: 0.985 AC: 15078 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3457 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4741 AN: 5178

South Asian (SAS) AF: 0.940 AC: 4536 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10611 AN: 10612

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67818 AN: 68042

Other (OTH) AF: 0.979 AC: 2067 AN: 2112

Alfa AF: 0.986 Hom.: 16044

Bravo AF: 0.968

Asia WGS AF: 0.924 AC: 3212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		0.016
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

Other links and lift over

dbSNP: rs710492; hg19: chr3-188694532;