Variant rs1556422538 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

Variant has been reported in ClinVar as Likely benign (★).

Frequency

Mitomap GenBank:

𝑓 0.0097 ( AC: 595 )

Consequence

RNR1
non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: 1.37

Variant links:

Genes affected

RNR1 (HGNC:):

RNR1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant M-1473-C-T is Benign according to our data. Variant chrM-1473-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 505288.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

High frequency in mitomap database: 0.0097

BS2

High AC in GnomadMitoHomoplasmic at 61

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNR1	unassigned_transcript_4786 use as main transcript	n.826C>T		non_coding_transcript_exon_variant	1/1
	use as main transcript

Ensembl

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

Frequencies

GnomAD4 exome

Cov.:

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

Mitomap GenBank

AF:

0.0097

AC:

595

Gnomad homoplasmic

AF:

0.0011

AC:

AN:

56434

Gnomad heteroplasmic

AF:

0.0

AC:

AN:

56434

Mitomap

No disease associated.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Aug 24, 2016

m.1473C>T in MTRNR1: This variant is not expected to have clinical significance because it has not been reported in individuals with hearing loss, and it has be en identified in 0.3% (4/1320) of human mitochondrial DNA sequences of the haplo group B4a (http://www.mitomap.org). Furthermore, 10 species have a thymine (T) a t this position, including 6 mammals (squirrel, Egyptian jerboa, prarie vole, Ch inese hamster, golden hamster, mouse). -

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.