dbSNP rs527236194: MT-CYB:p.Pro346Pro (chrM-15784-T-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP6_ModerateBP7BA1

The ENST00000361789.2(MT-CYB):c.1038T>C(p.Pro346Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:

𝑓 0.033 ( AC: 2012 )

Consequence

MT-CYB
ENST00000361789.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter P:1B:1

POAG---potential-for-association

Conservation

PhyloP100: -7.84

Publications

14 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:

TRNT (HGNC:7499): (mitochondrially encoded tRNA threonine)

TRNT links:

TRNP (HGNC:7494): (mitochondrially encoded tRNA proline)

TRNP Gene-Disease associations (from GenCC):

MERRF syndrome
Inheritance: Mitochondrial Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
mitochondrial disease
Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

TRNP links:

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new If you want to explore the variant's impact on the transcript ENST00000361789.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP6

Variant M-15784-T-C is Benign according to our data. Variant chrM-15784-T-C is described in ClinVar as Benign. ClinVar VariationId is 143899.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-7.84 with no splicing effect.

BA1

High frequency in mitomap database: 0.032899998

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.1038T>C	p.Pro346Pro	synonymous	Exon 1 of 1	ENSP00000354554.2	P00156
MT-TT	ENST00000387460.2	TSL:6	n.-104T>C		upstream_gene	N/A
MT-TP	ENST00000387461.2	TSL:6	n.*172A>G		downstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.033

AC:

2012

Gnomad homoplasmic

AF:

0.063

AC:

3527

AN:

56396

Gnomad heteroplasmic

AF:

0.00012

AC:

AN:

56396

Alfa

AF:

0.0421

Hom.:

2498

Mitomap

Disease(s): POAG---potential-for-association

Status: Reported

Publication(s):

24694284

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

Familial cancer of breast (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-7.8

Mutation Taster

=57/43

polymorphism

(source)

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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