rs10515153

Variant names:

• chr5-72693323-T-C
• rs10515153
• NR_186524.1:n.1469A>G

Variant summary

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

The NR_186524.1(TNPO1-DT):​n.1469A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0179 in 152,250 control chromosomes in the GnomAD database, including 68 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 0.018 (68 hom., cov: 32)
• Consequence: TNPO1-DT NR_186524.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 1 publications found

Genes affected

TNPO1-DT (HGNC:40328): (TNPO1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNPO1-DT	NR_186524.1	n.1469A>G		non_coding_transcript_exon_variant	Exon 6 of 6
TNPO1-DT	NR_105007.2	n.1221+228A>G		intron_variant	Intron 6 of 11
TNPO1-DT	NR_186510.1	n.1286+228A>G		intron_variant	Intron 7 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNPO1-DT	ENST00000507957.2	n.987-2619A>G		intron_variant	Intron 5 of 8	3
TNPO1-DT	ENST00000508217.3	n.471-2619A>G		intron_variant	Intron 4 of 8	3
TNPO1-DT	ENST00000512573.6	n.491-2619A>G		intron_variant	Intron 3 of 7	3

Frequencies

GnomAD3 genomes AF: 0.0179 AC: 2722 AN: 152132 Hom.: 68 Cov.: 32

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00193

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0179 AC: 2722 AN: 152250 Hom.: 68 Cov.: 32 AF XY: 0.0176 AC XY: 1309 AN XY: 74452

African (AFR) AF: 0.0543 AC: 2256 AN: 41556

American (AMR) AF: 0.0147 AC: 224 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0162 AC: 56 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00124 AC: 6 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00193 AC: 131 AN: 68012

Other (OTH) AF: 0.0171 AC: 36 AN: 2110

Alfa AF: 0.0160 Hom.: 8

Bravo AF: 0.0214

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.4
DANN	Benign	0.69
PhyloP100		0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10515153; hg19: chr5-71989150;