Genetic Variant ENST00000361789.2:c.58G>A (chrM-14804-G-A) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The ENST00000361789.2(MT-CYB):c.58G>A(p.Asp20Asn) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Mitomap GenBank:

𝑓 0.0 ( AC: 1 )

Consequence

MT-CYB
ENST00000361789.2 missense

Scores

Apogee2

Benign

0.24

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

No linked disesase in Mitomap

Conservation

PhyloP100: 7.53

Publications

0 publications found

Variant links:

Genes affected

MT-CYB (HGNC:7427): (mitochondrially encoded cytochrome b) Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including electron transport coupled proton transport; response to cobalamin; and response to glucagon. Located in mitochondrion. Implicated in ovarian carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

MT-CYB links:

MT-ND6 (HGNC:7462): (mitochondrially encoded NADH dehydrogenase 6) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Predicted to be located in mitochondrial inner membrane. Implicated in Leber hereditary optic neuropathy; Leigh disease; and spinal muscular atrophy with lower extremity predominante 2B. [provided by Alliance of Genome Resources, Apr 2022]

MT-ND6 links:

TRNE (HGNC:7479): (mitochondrially encoded tRNA glutamic acid)

TRNE Gene-Disease associations (from GenCC):

mitochondrial disease
Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

TRNE links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very low frequency in mitomap database: 0.0

BP4

Apogee2 supports a benign effect, 0.24369986 < 0.5 .

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361789.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MT-CYB	ENST00000361789.2	TSL:6	c.58G>A	p.Asp20Asn	missense	Exon 1 of 1	ENSP00000354554.2	P00156
MT-ND6	ENST00000361681.2	TSL:6	c.-131C>T		upstream_gene	N/A	ENSP00000354665.2	P03923
MT-TE	ENST00000387459.1	TSL:6	n.-62C>T		upstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.0

AC:

Gnomad homoplasmic

AF:

0.0

AC:

AN:

56426

Gnomad heteroplasmic

AF:

0.000018

AC:

AN:

56426

Mitomap

No disease associated.

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

Leigh syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

Apogee2

Benign

0.24

Hmtvar

Pathogenic

0.78

AlphaMissense

Uncertain

0.45

PhyloP100

7.5

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Mitomap

ClinVar

Computational scores

Publications

Other links and lift over