Variant M-14751-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2

The ENST00000361789.2(MT-CYB):c.5C>T(p.Thr2Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:

𝑓 0.00080 ( AC: 46 )

Consequence

MT-CYB
ENST00000361789.2 missense

Scores

Apogee2

Benign

0.046

Clinical Significance

Benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: 1.48

Variant links:

Genes affected

CYTB (HGNC:):

CYTB links:

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-CYB links:

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

MT-TE links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Apogee2 supports a benign effect, 0.045911513 < 0.5 .

BP6

Variant M-14751-C-T is Benign according to our data. Variant chrM-14751-C-T is described in ClinVar as [Benign]. Clinvar id is 693756.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomadMitoHomoplasmic at 24

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYTB	CYTB.1 use as main transcript	c.5C>T	p.Thr2Ile	missense_variant	1/1
TRNE	TRNE.1 use as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-CYB	ENST00000361789.2 linkuse as main transcript	c.5C>T	p.Thr2Ile	missense_variant	1/1			P1
MT-TE	ENST00000387459.1 linkuse as main transcript			upstream_gene_variant

Frequencies

GnomAD4 exome

Cov.:

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap GenBank

AF:

0.00080

AC:

Gnomad homoplasmic

AF:

0.00043

AC:

AN:

56432

Gnomad heteroplasmic

AF:

0.0

AC:

AN:

56432

Alfa

AF:

0.00111

Hom.:

Mitomap

No disease associated.

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

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.14751C>T (YP_003024038.1:p.Thr2Ile) 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: BS1, BS2, BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Apogee2

Benign

0.046

Hmtvar

Benign

0.27

AlphaMissense

Benign

0.11

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Mitomap

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over