rs41518645
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PS1_ModerateBP4BP6_ModerateBA1
The ENST00000361789.2(MT-CYB):c.511G>A(p.Asp171Asn) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Mitomap GenBank:
𝑓 0.015 ( AC: 934 )
Consequence
MT-CYB
ENST00000361789.2 missense
ENST00000361789.2 missense
Scores
Apogee2
Benign
Clinical Significance
LHON
Conservation
PhyloP100: 6.10
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PS1
?
Transcript ENST00000361789.2 (MT-CYB) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in UniProt
BP4
?
Apogee2 supports a benign effect, 0.17390026 < 0.5 .
BP6
?
Variant M-15257-G-A is Benign according to our data. Variant chrM-15257-G-A is described in ClinVar as [Benign]. Clinvar id is 9674.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
High frequency in mitomap database: 0.0153
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYTB | CYTB.1 use as main transcript | c.511G>A | p.Asp171Asn | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CYB | ENST00000361789.2 | c.511G>A | p.Asp171Asn | missense_variant | 1/1 | P1 |
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
934
Gnomad homoplasmic
AF:
AC:
719
AN:
56424
Gnomad heteroplasmic
AF:
AC:
1
AN:
56424
Alfa
AF:
Hom.:
Mitomap
LHON
ClinVar
Significance: Benign
Submissions summary: Pathogenic:1Uncertain:1Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leber optic atrophy Pathogenic:1Uncertain:1
Uncertain significance, no assertion criteria provided | curation | GeneReviews | Sep 19, 2013 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 01, 1996 | - - |
Leigh syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Oct 17, 2019 | The NC_012920.1:m.15257G>A (YP_003024038.1:p.Asp171Asn) variant in MTCYB gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BA1 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
Hmtvar
Benign
AlphaMissense
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at