rs199474826

Positions:

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:
𝑓 0.0 ( AC: 1 )

Consequence

COX2
missense

Scores

Apogee2
Benign
0.035

Clinical Significance

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

Conservation

PhyloP100: 0.257
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very low frequency in mitomap database: 0.0
BP6
Variant M-8009-G-A is Benign according to our data. Variant chrM-8009-G-A is described in ClinVar as [Benign]. Clinvar id is 9659.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COX2unassigned_transcript_4803 use as main transcriptc.424G>A p.Val142Ile missense_variant 1/1
use as main transcript

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0
AC:
1
Gnomad homoplasmic
AF:
0.0
AC:
0
AN:
56425
Gnomad heteroplasmic
AF:
0.000053
AC:
3
AN:
56425

Mitomap

No disease associated.

ClinVar

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

Submissions by phenotype

Familial colorectal cancer Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMNov 01, 1998- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingMendelicsMay 04, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
0.035
Hmtvar
Pathogenic
0.69
AlphaMissense
Benign
0.21
BayesDel_addAF
Benign
-0.35
T
DEOGEN2
Benign
0.0025
T
LIST_S2
Uncertain
0.94
D
MutationAssessor
Benign
0.64
N
PROVEAN
Benign
-0.17
N
Sift
Uncertain
0.0020
D
GERP RS
0.39
Varity_R
0.26

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: rs199474826; hg19: chrM-8010; API