3-12516442-ATATATGTGTG-A

Variant names:

• chr3-12516442-ATATATGTGTG-A
• rs1369917612
• NM_025265.4:c.910-167_910-158delATATGTGTGT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_025265.4(TSEN2):​c.910-167_910-158delATATGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.067 (260 hom., cov: 0)
• Consequence: TSEN2 NM_025265.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.779
• 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 3-12516442-ATATATGTGTG-A is Benign according to our data. Variant chr3-12516442-ATATATGTGTG-A is described in ClinVar as Benign. ClinVar VariationId is 1297382.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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.910-167_910-158delATATGTGTGT		intron	N/A	NP_079541.1	Q8NCE0-1
	TSEN2	NM_001321278.2		c.910-167_910-158delATATGTGTGT		intron	N/A	NP_001308207.1	C9J7Z4
	TSEN2	NM_001145392.2		c.910-167_910-158delATATGTGTGT		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.910-168_910-159delTATATGTGTG		intron	N/A	ENSP00000284995.6	Q8NCE0-1
	TSEN2	ENST00000402228.7	TSL:1	c.910-168_910-159delTATATGTGTG		intron	N/A	ENSP00000385976.3	Q8NCE0-1
	TSEN2	ENST00000454502.6	TSL:1	c.733-168_733-159delTATATGTGTG		intron	N/A	ENSP00000392029.2	Q8NCE0-4

Frequencies

GnomAD3 genomes AF: 0.0669 AC: 5954 AN: 89024 Hom.: 262 Cov.: 0

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0428

Gnomad ASJ AF: 0.00219

Gnomad EAS AF: 0.000712

Gnomad SAS AF: 0.00789

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0275

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.0706

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

GnomAD4 genome AF: 0.0669 AC: 5959 AN: 89102 Hom.: 260 Cov.: 0 AF XY: 0.0654 AC XY: 2801 AN XY: 42798

African (AFR) AF: 0.163 AC: 3991 AN: 24476

American (AMR) AF: 0.0426 AC: 307 AN: 7214

Ashkenazi Jewish (ASJ) AF: 0.00219 AC: 5 AN: 2278

East Asian (EAS) AF: 0.000712 AC: 2 AN: 2808

South Asian (SAS) AF: 0.00791 AC: 20 AN: 2530

European-Finnish (FIN) AF: 0.0436 AC: 261 AN: 5986

Middle Eastern (MID) AF: 0.0301 AC: 5 AN: 166

European-Non Finnish (NFE) AF: 0.0280 AC: 1171 AN: 41760

Other (OTH) AF: 0.0691 AC: 81 AN: 1172

Alfa AF: 0.0362 Hom.: 1

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		0.78
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1369917612; hg19: chr3-12557941;