chrM-15511-T-C

Position:

• chrM-15511-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.765T>C​(p.Asn255=) 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 0.0026 (AC: 158)
• Consequence: MT-CYB ENST00000361789.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter P:1 B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: 0.352

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-15511-T-C is Benign according to our data. Variant chrM-15511-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 143893.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.352 with no splicing effect.
• BS2: High AC in GnomadMitoHomoplasmic at 187

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYTB	CYTB.1	c.765T>C	p.Asn255=	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.765T>C	p.Asn255=	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: 0.0026 AC: 158

Gnomad homoplasmic AF: 0.0033 AC: 187 AN: 56421

Gnomad heteroplasmic AF: 0.00011 AC: 6 AN: 56421

Alfa AF: 0.00334 Hom.: 15

Mitomap

No disease associated.

ClinVar

Significance: Likely benign

Submissions summary: Pathogenic:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Ovarian neoplasm Pathogenic:1

Likely pathogenic, no assertion criteria provided

literature only

Department of Zoology Govt. MVM College

-

- -

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

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

Mar 18, 2016

- -

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: rs527236188; hg19: chrM-15512;