3-12516439-AAAATATATG-A

Position:

• chr3-12516439-AAAATATATG-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_025265.4(TSEN2):​c.910-171_910-163delAAATATATG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (518 hom., cov: 0)
• Consequence: TSEN2 NM_025265.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.02

Genes affected

TSEN2 (HGNC:28422): (tRNA splicing endonuclease subunit 2) This gene encodes one of the subunits of the tRNA splicing endonuclease. This endonuclease catalyzes the first step in RNA splicing which is the removal of introns. Mutations in this gene have been associated with pontocerebellar hypoplasia type 2. A pseudogene has been identified on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2009]

TSEN2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-12516439-AAAATATATG-A is Benign according to our data. Variant chr3-12516439-AAAATATATG-A is described in ClinVar as [Benign]. Clinvar id is 1239795.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSEN2	NM_025265.4	c.910-171_910-163delAAATATATG		intron_variant		ENST00000284995.11	NP_079541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSEN2	ENST00000284995.11	c.910-171_910-163delAAATATATG		intron_variant		1	NM_025265.4	ENSP00000284995.6

Frequencies

GnomAD3 genomes AF: 0.152 AC: 11175 AN: 73662 Hom.: 518 Cov.: 0

Gnomad AFR AF: 0.0625

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0572

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.152 AC: 11170 AN: 73724 Hom.: 518 Cov.: 0 AF XY: 0.152 AC XY: 5377 AN XY: 35286

Gnomad4 AFR AF: 0.0623

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0566

Gnomad4 SAS AF: 0.0683

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.195

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs369155945; hg19: chr3-12557938;