Variant 10-103394332-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000337003.4(ATP5MK):c.-143T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 533,164 control chromosomes in the GnomAD database, including 32,579 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.27 ( 6595 hom., cov: 32)

Exomes 𝑓: 0.36 ( 25984 hom. )

Consequence

ATP5MK
ENST00000337003.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Variant links:

Genes affected

ATP5MK (HGNC:30889): (ATP synthase membrane subunit k) Located in mitochondrion. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in mitochondrial complex V (ATP synthase) deficiency nuclear type 6. [provided by Alliance of Genome Resources, Apr 2022]

ATP5MK links:

MIR1307 (HGNC:35372): (microRNA 1307) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR1307 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP5MK	NM_001206427.2 linkuse as main transcript	c.-10+1414T>C		intron_variant		ENST00000369815.6	NP_001193356.1
MIR1307	NR_031707.1 linkuse as main transcript	n.70T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP5MK	ENST00000369815.6 linkuse as main transcript	c.-10+1414T>C		intron_variant		2	NM_001206427.2	ENSP00000358830	P1
MIR1307	ENST00000408840.1 linkuse as main transcript	n.70T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

40989

AN:

151960

Hom.:

6591

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0924

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.307

Gnomad EAS

AF:

0.349

Gnomad SAS

AF:

0.502

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.328

Gnomad OTH

AF:

0.277

GnomAD3 exomes

AF:

0.340

AC:

84712

AN:

249002

Hom.:

15534

AF XY:

0.353

AC XY:

47787

AN XY:

135320

show subpopulations

Gnomad AFR exome

AF:

0.0866

Gnomad AMR exome

AF:

0.307

Gnomad ASJ exome

AF:

0.310

Gnomad EAS exome

AF:

0.344

Gnomad SAS exome

AF:

0.508

Gnomad FIN exome

AF:

0.399

Gnomad NFE exome

AF:

0.331

Gnomad OTH exome

AF:

0.337

GnomAD4 exome

AF:

0.357

AC:

136113

AN:

381088

Hom.:

25984

Cov.:

AF XY:

0.371

AC XY:

80428

AN XY:

216808

show subpopulations

Gnomad4 AFR exome

AF:

0.0890

Gnomad4 AMR exome

AF:

0.308

Gnomad4 ASJ exome

AF:

0.312

Gnomad4 EAS exome

AF:

0.338

Gnomad4 SAS exome

AF:

0.508

Gnomad4 FIN exome

AF:

0.397

Gnomad4 NFE exome

AF:

0.330

Gnomad4 OTH exome

AF:

0.324

GnomAD4 genome

AF:

0.270

AC:

40995

AN:

152076

Hom.:

6595

Cov.:

AF XY:

0.276

AC XY:

20536

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.0922

Gnomad4 AMR

AF:

0.296

Gnomad4 ASJ

AF:

0.307

Gnomad4 EAS

AF:

0.350

Gnomad4 SAS

AF:

0.503

Gnomad4 FIN

AF:

0.400

Gnomad4 NFE

AF:

0.328

Gnomad4 OTH

AF:

0.277

Alfa

AF:

0.313

Hom.:

10178

Bravo

AF:

0.250

Asia WGS

AF:

0.392

AC:

1361

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.91

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over