rs41487950

Positions:

• chrM-10084-T-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BS1 BS2

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

• Frequency: Mitomap GenBank: 𝑓 0.0090 (AC: 552)
• Consequence: ND3 missense
• Scores: Apogee2 Benign 0.052
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3 No linked disesase in Mitomap
• Conservation: PhyloP100: -0.638

Genes affected

ND3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant M-10084-T-C is Benign according to our data. Variant chrM-10084-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 235627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: High frequency in mitomap database: 0.009
• BS2: High AC in GnomadMitoHomoplasmic at 292

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ND3	unassigned_transcript_4809	c.26T>C	p.Ile9Thr	missense_variant	1/1
TRNG	unassigned_transcript_4808	c.*26T>C		downstream_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: 0.0090 AC: 552

Gnomad homoplasmic AF: 0.0052 AC: 292 AN: 56418

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56418

Alfa AF: 0.00536 Hom.: 229

Mitomap

No disease associated.

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Aug 12, 2015	- -

Leigh syndrome Benign:1

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.10084T>C (YP_003024033.1:p.Ile9Thr) variant in MTND3 gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BA1 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Apogee2	Benign	0.052
Hmtvar	Benign	0.10
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.45	T
DEOGEN2	Benign	0.037	T
LIST_S2	Benign	0.59	T
MutationAssessor	Benign	1.1	L
PROVEAN	Benign	-0.96	N
Sift	Benign	0.51	T
Sift4G	Benign	0.34	T
GERP RS		-2.0
Varity_R		0.059

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41487950; hg19: chrM-10085;