rs201250154

Positions:

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BS1BS2

The ENST00000361789.2(MT-CYB):ā€‹c.489A>Gā€‹(p.Trp163=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (ā˜…).

Frequency

Mitomap GenBank:
š‘“ 0.0093 ( AC: 568 )

Consequence

MT-CYB
ENST00000361789.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1
No linked disesase in Mitomap

Conservation

PhyloP100: 2.22
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP6
Variant M-15235-A-G is Benign according to our data. Variant chrM-15235-A-G is described in ClinVar as [Benign]. Clinvar id is 377041.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.22 with no splicing effect.
BS1
High frequency in mitomap database: 0.0093
BS2
High AC in GnomadMitoHomoplasmic at 58

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYTBCYTB.1 use as main transcriptc.489A>G p.Trp163= synonymous_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-CYBENST00000361789.2 linkuse as main transcriptc.489A>G p.Trp163= 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:
0.0093
AC:
568
Gnomad homoplasmic
AF:
0.0010
AC:
58
AN:
56434
Gnomad heteroplasmic
AF:
0.0
AC:
0
AN:
56434

Mitomap

No disease associated.

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingCenter for Pediatric Genomic Medicine, Children's Mercy Hospital and ClinicsJan 03, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201250154; hg19: chrM-15236; API