M-3336-T-G

Position:

• chrM-3336-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Mitomap GenBank: Absent
• Consequence: ND1 missense
• Scores: Apogee2 Benign 0.26
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: -5.56

Genes affected

ND1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: No frequency data in Mitomap. Probably very rare.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ND1	unassigned_transcript_4790	c.30T>G	p.Ile10Met	missense_variant	1/1
TRNL1	unassigned_transcript_4789	c.*32T>G		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

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Apogee2	Benign	0.26
Hmtvar	Pathogenic	0.58
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.53	T
DEOGEN2	Benign	0.043	T
LIST_S2	Benign	0.80	T
MutationAssessor	Benign	1.2	L
PROVEAN	Benign	-1.9	N
Sift4G	Uncertain	0.049	D
GERP RS		-4.0
Varity_R		0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28416101; hg19: chrM-3337;