rs971572

chr1-184099374-C-Achr1-184099374-C-G

Variant summary

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

The ENST00000664793.1(ENSG00000286655):n.68-16489G>T variant causes a intron, non coding transcript 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: ENST00000664793.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901

Genes affected

(HGNC:):

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]

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664793.1	n.68-16489G>T		intron_variant, non_coding_transcript_variant
TSEN15	ENST00000643916.1	c.*116-13491C>A		intron_variant, NMD_transcript_variant
TSEN15	ENST00000644592.1	c.354-20346C>A		intron_variant, NMD_transcript_variant

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;