1-184099374-C-A

Variant names:

• chr1-184099374-C-A
• rs971572
• ENST00000643916.1:n.*116-13491C>A

Variant summary

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

The ENST00000644592.1(TSEN15):​n.354-20346C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,802 control chromosomes in the GnomAD database, including 7,911 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 0.31 (7911 hom., cov: 31)
• Consequence: TSEN15 ENST00000644592.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901

Genes affected

TSEN15 (HGNC:16791): (tRNA splicing endonuclease subunit 15) This gene encodes a subunit of the tRNA splicing endonuclease, which catalyzes the removal of introns from tRNA precursors. Alternative splicing results in multiple transcript variants. There is a pseudogene of this gene on chromosome 17. [provided by RefSeq, Jul 2014]

ENSG00000286655 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.561 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
TSEN15	ENST00000643916.1	n.*116-13491C>A		intron_variant	Intron 2 of 4			ENSP00000494533.1
TSEN15	ENST00000644592.1	n.354-20346C>A		intron_variant	Intron 3 of 5			ENSP00000495621.1
ENSG00000286655	ENST00000664793.1	n.68-16489G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46410 AN: 151684 Hom.: 7911 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.306 AC: 46426 AN: 151802 Hom.: 7911 Cov.: 31 AF XY: 0.310 AC XY: 22967 AN XY: 74180

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.302

Alfa AF: 0.334 Hom.: 10972

Bravo AF: 0.293

Asia WGS AF: 0.416 AC: 1447 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	8.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs971572; hg19: chr1-184068508; COSMIC: COSV59996059;