NM_025265.4:c.910-171_910-163delAAATATATG

Variant names:

• chr3-12516439-AAAATATATG-A
• rs369155945
• NM_025265.4:c.910-171_910-163delAAATATATG

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

MKRN2OS (HGNC:40375): (MKRN2 opposite strand)

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025265.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSEN2	NM_025265.4	MANE Select	c.910-171_910-163delAAATATATG		intron	N/A	NP_079541.1	Q8NCE0-1
	TSEN2	NM_001321278.2		c.910-171_910-163delAAATATATG		intron	N/A	NP_001308207.1	C9J7Z4
	TSEN2	NM_001145392.2		c.910-171_910-163delAAATATATG		intron	N/A	NP_001138864.1	Q8NCE0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSEN2	ENST00000284995.11	TSL:1 MANE Select	c.910-171_910-163delAAATATATG		intron	N/A	ENSP00000284995.6	Q8NCE0-1
	TSEN2	ENST00000402228.7	TSL:1	c.910-171_910-163delAAATATATG		intron	N/A	ENSP00000385976.3	Q8NCE0-1
	TSEN2	ENST00000454502.6	TSL:1	c.733-171_733-163delAAATATATG		intron	N/A	ENSP00000392029.2	Q8NCE0-4

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

African (AFR) AF: 0.0623 AC: 824 AN: 13236

American (AMR) AF: 0.196 AC: 1453 AN: 7416

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 283 AN: 1876

East Asian (EAS) AF: 0.0566 AC: 203 AN: 3584

South Asian (SAS) AF: 0.0683 AC: 168 AN: 2458

European-Finnish (FIN) AF: 0.200 AC: 1064 AN: 5312

Middle Eastern (MID) AF: 0.165 AC: 33 AN: 200

European-Non Finnish (NFE) AF: 0.181 AC: 6907 AN: 38226

Other (OTH) AF: 0.195 AC: 191 AN: 982

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.0
Mutation Taster		=16/84	disease causing

Splicing

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

Other links and lift over

dbSNP: rs369155945; hg19: chr3-12557938;