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GeneBe

rs1556422496

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000389680.2(MT-RNR1):n.307C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:
𝑓 0.00040 ( AC: 22 )

Consequence

MT-RNR1
ENST00000389680.2 non_coding_transcript_exon

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.13
Variant links:
Genes affected
MT-RNR1 (HGNC:7470): (mitochondrially encoded 12S RNA) Enables DNA binding activity and DNA-binding transcription factor binding activity. Involved in several processes, including osteoblast proliferation; regulation of carbohydrate utilization; and regulation of phosphate metabolic process. Located in extracellular space; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6
Variant M-954-C-T is Benign according to our data. Variant chrM-954-C-T is described in ClinVar as [Benign]. Clinvar id is 517632.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomadMitoHomoplasmic at 49

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNR1RNR1.1 use as main transcriptn.307C>T non_coding_transcript_exon_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-RNR1ENST00000389680.2 linkuse as main transcriptn.307C>T non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.00040
AC:
22
Gnomad homoplasmic
AF:
0.00087
AC:
49
AN:
56434
Gnomad heteroplasmic
AF:
0.000018
AC:
1
AN:
56434

Mitomap

No disease associated.

ClinVar

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

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineNov 27, 2017m.954C>T in MTRNR1: This variant is not expected to have clinical significance b ecause it has been identified in 48% (6/14) of the L2e haplogroup in MitoMap (ht tps://www.mitomap.org). -

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.

Other links and lift over

dbSNP: rs1556422496; hg19: chrM-956; API