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GeneBe

M-14783-T-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BA1

The ENST00000361789.2(MT-CYB):c.37T>C(p.Leu13=) 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 0.20 ( AC: 12413 )

Consequence

MT-CYB
ENST00000361789.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter P:1B:1
Possible-role-in-high-altitude-sickness

Conservation

PhyloP100: 3.18
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-TE (HGNC:7479): (mitochondrially encoded tRNA glutamic acid)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant M-14783-T-C is Benign according to our data. Variant chrM-14783-T-C is described in ClinVar as [Benign]. Clinvar id is 140588.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=3.18 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
High frequency in mitomap database: 0.203

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYTBCYTB.1 use as main transcriptc.37T>C p.Leu13= synonymous_variant 1/1
TRNETRNE.1 use as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-CYBENST00000361789.2 linkuse as main transcriptc.37T>C p.Leu13= synonymous_variant 1/1 P1
MT-TEENST00000387459.1 linkuse as main transcript upstream_gene_variant

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.20
AC:
12413
Gnomad homoplasmic
AF:
0.055
AC:
3118
AN:
56336
Gnomad heteroplasmic
AF:
0.000053
AC:
3
AN:
56336
Alfa
AF:
0.0205
Hom.:
168

Mitomap

Possible-role-in-high-altitude-sickness

ClinVar

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

Submissions by phenotype

Familial cancer of breast Pathogenic:1Benign:1
Likely pathogenic, no assertion criteria providedliterature onlyDepartment of Zoology Govt. MVM College-- -
Benign, criteria provided, single submittercurationOphthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology BaselAug 29, 2023Clinical significance based on ACMG v2.0 -

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: rs193302982; hg19: chrM-14784; API