M-750-A-G

Position:

• chrM-750-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

Variant has been reported in ClinVar as association not found (no stars).

• Frequency: Mitomap GenBank: 𝑓 0.98 (AC: 60110)
• Consequence: RNR1 non_coding_transcript_exon
• Clinical Significance: association not found no assertion criteria provided O:2 No linked disesase in Mitomap
• Conservation: PhyloP100: 6.91

Genes affected

RNR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: High frequency in mitomap database: 0.9832

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNR1	unassigned_transcript_4786	n.103A>G		non_coding_transcript_exon_variant	1/1

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: 0.98 AC: 60110

Gnomad homoplasmic AF: 0.98 AC: 55419 AN: 56354

Gnomad heteroplasmic AF: 0.00011 AC: 6 AN: 56354

Alfa AF: 0.970 Hom.: 228

Mitomap

No disease associated.

ClinVar

Significance: association not found

Submissions summary: Other:2

Revision: no assertion criteria provided

Submissions by phenotype

Venous thromboembolism Other:1

association not found, no assertion criteria provided

case-control

Genomics Division, Defence Institute of Physiology and Allied Sciences

-

Three age and sex matched study groups were taken and whole exome sequencing was performed. 1. Healthy Subjects (n=19) 2. Sea Level Venous Thromboembolism (n=15) 3. High Altitude Venous Thromboembolism (n=6). Nature of this variant is not provided. After analysis, it was found that rs2853518 is present in all study groups. First time it is being reported that there is association of rs28535138 with Venous thromboembolism. -

not provided Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853518; hg19: chrM-752;