ENST00000569473.1:n.108T>C

Variant names:

• chr15-89335160-T-C
• rs2856268
• ENST00000569473.1:n.108T>C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000569473.1(POLG-DT):​n.108T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,144 control chromosomes in the GnomAD database, including 9,456 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.34 (9456 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: POLG-DT ENST00000569473.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -7.58

Genes affected

POLG-DT (HGNC:55363): (POLG divergent transcript)

TRR-TCG1-1 (HGNC:34827):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP6: Variant 15-89335160-T-C is Benign according to our data. Variant chr15-89335160-T-C is described in ClinVar as [Benign]. Clinvar id is 695736.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLG-DT	NR_186332.1	n.369-27T>C		intron_variant	Intron 1 of 1
TRR-TCG1-1	unassigned_transcript_2746	c.*15T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLG-DT	ENST00000569473.1	n.108T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
POLG-DT	ENST00000562356.1	n.-111T>C		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51608 AN: 152022 Hom.: 9451 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.334

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.250

GnomAD4 genome AF: 0.339 AC: 51622 AN: 152140 Hom.: 9456 Cov.: 32 AF XY: 0.346 AC XY: 25756 AN XY: 74368

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.331

Alfa AF: 0.244 Hom.: 753

Bravo AF: 0.326

Asia WGS AF: 0.340 AC: 1181 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Oct 03, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 22684821) -

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Progressive sclerosing poliodystrophy Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	0.0020
DANN	Benign	0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2856268; hg19: chr15-89878391;