rs1450118

Variant names:

• chr3-189218969-A-G
• rs1450118
• NM_198485.4:c.302+3586A>G

Variant summary

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

The NM_198485.4(TPRG1):​c.302+3586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,950 control chromosomes in the GnomAD database, including 21,923 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 0.54 (21923 hom., cov: 31)
• Consequence: TPRG1 NM_198485.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPRG1	NM_198485.4	c.302+3586A>G		intron_variant	Intron 3 of 5	ENST00000345063.8	NP_940887.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPRG1	ENST00000345063.8	c.302+3586A>G		intron_variant	Intron 3 of 5	1	NM_198485.4	ENSP00000341031.3

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81451 AN: 151832 Hom.: 21898 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.536 AC: 81517 AN: 151950 Hom.: 21923 Cov.: 31 AF XY: 0.534 AC XY: 39644 AN XY: 74250

African (AFR) AF: 0.478 AC: 19813 AN: 41432

American (AMR) AF: 0.572 AC: 8738 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3018 AN: 5158

South Asian (SAS) AF: 0.639 AC: 3080 AN: 4822

European-Finnish (FIN) AF: 0.551 AC: 5806 AN: 10540

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37277 AN: 67942

Other (OTH) AF: 0.573 AC: 1207 AN: 2108

Alfa AF: 0.549 Hom.: 19280

Bravo AF: 0.533

Asia WGS AF: 0.615 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.71
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: rs1450118; hg19: chr3-188936758;