rs41453547

Positions:

• chrM-5656-A-G

Variant summary

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

The M-5656-A-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Mitomap GenBank: 𝑓 0.012 (AC: 748)
• Consequence: MT-TA ENST00000387392.1 upstream_gene
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: -2.98

Genes affected

MT-TA (HGNC:7475): (mitochondrially encoded tRNA alanine)

TRNA (HGNC:):

MT-TN (HGNC:7493): (mitochondrially encoded tRNA asparagine)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: High frequency in mitomap database: 0.012200001

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRNA	TRNA.1			upstream_gene_variant
TRNN	TRNN.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-TA	ENST00000387392.1			upstream_gene_variant
MT-TN	ENST00000387400.1			downstream_gene_variant

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.012 AC: 748

Gnomad homoplasmic AF: 0.021 AC: 1171 AN: 56424

Gnomad heteroplasmic AF: 0.0 AC: 0 AN: 56424

Alfa AF: 0.0130 Hom.: 48

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

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: rs41453547; hg19: chrM-5657;