7-129028456-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012470.4(TNPO3):c.121-10299A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,898 control chromosomes in the GnomAD database, including 26,901 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 0.59 (26901 hom., cov: 32)
• Consequence: TNPO3 NM_012470.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

TNPO3 (HGNC:17103): (transportin 3) The protein encoded by this gene is a nuclear import receptor for serine/arginine-rich (SR) proteins such as the splicing factors SFRS1 and SFRS2. The encoded protein has also been shown to be involved in HIV-1 infection, apparently through interaction with the HIV-1 capsid protein. Several protein-coding and non-coding transcript variants have been found for this gene. [provided by RefSeq, Apr 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNPO3	NM_012470.4	c.121-10299A>C		intron_variant		ENST00000265388.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNPO3	ENST00000265388.10	c.121-10299A>C		intron_variant		1	NM_012470.4	P1

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90030 AN: 151780 Hom.: 26876 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.593 AC: 90102 AN: 151898 Hom.: 26901 Cov.: 32 AF XY: 0.591 AC XY: 43856 AN XY: 74210

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.607

Alfa AF: 0.609 Hom.: 55424

Bravo AF: 0.587

Asia WGS AF: 0.541 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.2
Dann	Benign	0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs10239340; hg19: chr7-128668510;