3-12516442-ATATATG-A

Position:

• chr3-12516442-ATATATG-A

Variant summary

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

The NM_025265.4(TSEN2):​c.910-167_910-162delATATGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.21 (1258 hom., cov: 0)
• Consequence: TSEN2 NM_025265.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.779

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

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-12516442-ATATATG-A is Benign according to our data. Variant chr3-12516442-ATATATG-A is described in ClinVar as [Benign]. Clinvar id is 1265447.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSEN2	NM_025265.4	c.910-167_910-162delATATGT		intron_variant		ENST00000284995.11	NP_079541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSEN2	ENST00000284995.11	c.910-168_910-163delTATATG		intron_variant		1	NM_025265.4	ENSP00000284995.6

Frequencies

GnomAD3 genomes AF: 0.209 AC: 18581 AN: 88830 Hom.: 1258 Cov.: 0

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.209 AC: 18582 AN: 88906 Hom.: 1258 Cov.: 0 AF XY: 0.215 AC XY: 9181 AN XY: 42668

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.195

Alfa AF: 0.117 Hom.: 1

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

Aug 25, 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: rs370112322; hg19: chr3-12557941;