Genetic Variant MT-CYB:p.Ser172Ser (chrM-15262-T-C) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP6_ModerateBP7BS2

The ENST00000361789.2(MT-CYB):c.516T>C(p.Ser172Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Mitomap GenBank:

𝑓 0.0038 ( AC: 232 )

Consequence

MT-CYB
ENST00000361789.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: -0.0350

Publications

3 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 Gene-Disease associations (from GenCC):

mitochondrial disease
Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
mitochondrial complex III deficiency
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Leber hereditary optic neuropathy
Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet

MT-CYB 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 -7 ACMG points.

BP6

Variant M-15262-T-C is Benign according to our data. Variant chrM-15262-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 376959.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.035 with no splicing effect.

BS2

High AC in GnomadMitoHomoplasmic at 81

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-CYB	ENST00000361789.2	TSL:6	c.516T>C	p.Ser172Ser	synonymous	Exon 1 of 1	ENSP00000354554.2	P00156

Frequencies

Mitomap GenBank

AF:

0.0038

AC:

232

Gnomad homoplasmic

AF:

0.0014

AC:

AN:

56412

Gnomad heteroplasmic

AF:

0.000071

AC:

AN:

56412

Alfa

AF:

0.000668

Hom.:

Mitomap

No disease associated.

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.035

Mutation Taster

=100/0

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