rs527236194

Positions:

• chrM-15784-T-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_Moderate BP7 BA1

The ENST00000361789.2(MT-CYB):​c.1038T>C​(p.Pro346=) 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
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1 POAG---potential-for-association
• Conservation: PhyloP100: -7.84

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 -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 id 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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYTB	CYTB.1	c.1038T>C	p.Pro346=	synonymous_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-CYB	ENST00000361789.2	c.1038T>C	p.Pro346=	synonymous_variant	1/1			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: 0.033 AC: 2012

Gnomad homoplasmic AF: 0.063 AC: 3527 AN: 56396

Gnomad heteroplasmic AF: 0.00012 AC: 7 AN: 56396

Alfa AF: 0.0134 Hom.: 549

Mitomap

POAG---potential-for-association

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial cancer of breast Pathogenic:1 Benign:1

Benign, criteria provided, single submitter	curation	Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel	Aug 29, 2023	Clinical significance based on ACMG v2.0 -
Likely pathogenic, no assertion criteria provided	literature only	Department of Zoology Govt. MVM College	-	- -

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: rs527236194; hg19: chrM-15785;