chrM-10398-A-T

Position:

• chrM-10398-A-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.00010 (AC: 7)
• Consequence: ND3 missense
• Scores: Apogee2 Benign 0.022
• Clinical Significance: Likely benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -0.338

Genes affected

ND3 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant M-10398-A-T is Benign according to our data. Variant chrM-10398-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 693288.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 13

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ND3	unassigned_transcript_4809	c.340A>T	p.Thr114Ser	missense_variant	1/1
TRNR	unassigned_transcript_4810	c.-7A>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.00010 AC: 7

Gnomad homoplasmic AF: 0.00023 AC: 13 AN: 56433

Gnomad heteroplasmic AF: 0.0 AC: 0 AN: 56433

Alfa AF: 0.000110 Hom.: 6166

Mitomap

No disease associated.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Leigh syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

Oct 17, 2019

The NC_012920.1:m.10398A>T (YP_003024033.1:p.Thr114Ser) variant in MTND3 gene is interpretated to be a Likely Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BS1, BP4 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Apogee2	Benign	0.022
Hmtvar	Benign	0.090
AlphaMissense	Benign	0.095
DEOGEN2	Benign	0.18	T
LIST_S2	Benign	0.68	T
MutationAssessor	Benign	0.34	N
PROVEAN	Benign	-1.4	N
Sift	Benign	0.070	T
Sift4G	Uncertain	0.054	T

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853826; hg19: chrM-10399;