chrM-15470-T-C

Position:

• chrM-15470-T-C

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP6_Moderate BP7 BS2

The ENST00000361789.2(MT-CYB):​c.724T>C​(p.Leu242=) 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 0.0014 (AC: 87)
• Consequence: MT-CYB ENST00000361789.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -0.540

Genes affected

CYTB (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP6: Variant M-15470-T-C is Benign according to our data. Variant chrM-15470-T-C is described in ClinVar as [Benign]. Clinvar id is 143892.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.54 with no splicing effect.
• BS2: High AC in GnomadMitoHomoplasmic at 92

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYTB	CYTB.1	c.724T>C	p.Leu242=	synonymous_variant	1/1		YP_003024038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-CYB	ENST00000361789.2	c.724T>C	p.Leu242=	synonymous_variant	1/1			ENSP00000354554	P1

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.0014 AC: 87

Gnomad homoplasmic AF: 0.0016 AC: 92 AN: 56425

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56425

Alfa AF: 0.000890 Hom.: 4

Mitomap

No disease associated.

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial cancer of breast Pathogenic:1

Likely pathogenic, no assertion criteria provided

literature only

Department of Zoology Govt. MVM College

-

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Sep 17, 2015

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs527236187; hg19: chrM-15471;