Variant chrM-12372-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

Variant has been reported in ClinVar as Benign (★★).

Frequency

Mitomap GenBank:

𝑓 0.14 ( AC: 8474 )

Consequence

ND5
synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Altered-brain-pH-/-sCJD-patients

Conservation

PhyloP100: -5.07

Variant links:

Genes affected

ND5 (HGNC:):

ND5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant M-12372-G-A is Benign according to our data. Variant chrM-12372-G-A is described in ClinVar as [Benign]. Clinvar id is 522717.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

High frequency in mitomap database: 0.13859999

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons
ND5	unassigned_transcript_4816 use as main transcript	c.36G>A	p.Leu12Leu	synonymous_variant	1/1
TRNL2	unassigned_transcript_4815 use as main transcript	c.*36G>A		downstream_gene_variant
	use as main transcript

Ensembl

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

Frequencies

GnomAD4 exome

Cov.:

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

Mitomap GenBank

AF:

0.14

AC:

8474

Gnomad homoplasmic

AF:

0.16

AC:

8901

AN:

56353

Gnomad heteroplasmic

AF:

0.00014

AC:

AN:

56353

Alfa

AF:

0.259

Hom.:

1173

Mitomap

Altered-brain-pH-/-sCJD-patients

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

Mitochondrial disease

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genomic Research Center, Shahid Beheshti University of Medical Sciences

Jul 20, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.