Variant rs1962412 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_005175.3(ATP5MC1):c.-23T>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 0.644 in 156,470 control chromosomes in the GnomAD database, including 33,187 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 0.64 ( 31906 hom., cov: 29)

Exomes 𝑓: 0.71 ( 1281 hom. )

Consequence

ATP5MC1
NM_005175.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.918

Variant links:

Genes affected

ATP5MC1 (HGNC:841): (ATP synthase membrane subunit c locus 1) This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene is one of three genes that encode subunit c of the proton channel. Each of the three genes have distinct mitochondrial import sequences but encode the identical mature protein. Alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Jul 2008]

ATP5MC1 links:

ATP5MC1 (HGNC:):

ATP5MC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
ATP5MC1	NM_005175.3 linkuse as main transcript	c.-23T>C	5_prime_UTR_variant	1/5	ENST00000393366.7	NP_005166.1	P05496Q6FIH7
ATP5MC1	NM_001002027.2 linkuse as main transcript	c.-10+57T>C	intron_variant			NP_001002027.1	P05496Q6FIH7
LOC105371814	NR_135674.1 linkuse as main transcript	n.46-220A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP5MC1	ENST00000393366.7 linkuse as main transcript	c.-23T>C		5_prime_UTR_variant	1/5	1	NM_005175.3	ENSP00000377033.2		P05496

Frequencies

GnomAD3 genomes

AF:

0.642

AC:

97224

AN:

151384

Hom.:

31900

Cov.:

show subpopulations

Gnomad AFR

AF:

0.529

Gnomad AMI

AF:

0.720

Gnomad AMR

AF:

0.548

Gnomad ASJ

AF:

0.588

Gnomad EAS

AF:

0.840

Gnomad SAS

AF:

0.726

Gnomad FIN

AF:

0.740

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.698

Gnomad OTH

AF:

0.651

GnomAD4 exome

AF:

0.713

AC:

3540

AN:

4968

Hom.:

1281

Cov.:

AF XY:

0.711

AC XY:

2281

AN XY:

3206

show subpopulations

Gnomad4 AFR exome

AF:

0.542

Gnomad4 AMR exome

AF:

0.549

Gnomad4 ASJ exome

AF:

0.519

Gnomad4 EAS exome

AF:

0.827

Gnomad4 SAS exome

AF:

0.713

Gnomad4 FIN exome

AF:

0.736

Gnomad4 NFE exome

AF:

0.729

Gnomad4 OTH exome

AF:

0.726

GnomAD4 genome

AF:

0.642

AC:

97261

AN:

151502

Hom.:

31906

Cov.:

AF XY:

0.642

AC XY:

47518

AN XY:

73982

show subpopulations

Gnomad4 AFR

AF:

0.529

Gnomad4 AMR

AF:

0.547

Gnomad4 ASJ

AF:

0.588

Gnomad4 EAS

AF:

0.840

Gnomad4 SAS

AF:

0.726

Gnomad4 FIN

AF:

0.740

Gnomad4 NFE

AF:

0.698

Gnomad4 OTH

AF:

0.652

Alfa

AF:

0.677

Hom.:

25066

Bravo

AF:

0.623

Asia WGS

AF:

0.755

AC:

2622

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

DANN

Benign

0.88

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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