chr10-7807725-T-C

Variant names:

• chr10-7807725-T-C
• rs4655
• NM_001001973.3:c.*97T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001973.3(ATP5F1C):​c.*97T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 1,557,388 control chromosomes in the GnomAD database, including 103,286 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 0.35 (9230 hom., cov: 32)
  • Exomes 𝑓: 0.36 (94056 hom.)
• Consequence: ATP5F1C NM_001001973.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 17 publications found

Genes affected

ATP5F1C (HGNC:833): (ATP synthase F1 subunit gamma) 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 consists of three main subunits (a, b, c). This gene encodes the gamma subunit of the catalytic core. Alternatively spliced transcript variants encoding different isoforms have been identified. This gene also has a pseudogene on chromosome 14. [provided by RefSeq, Jul 2008]

ENSG00000305746 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001973.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP5F1C	NM_001001973.3	MANE Select	c.*97T>C		3_prime_UTR	Exon 10 of 10	NP_001001973.1
	ATP5F1C	NM_005174.4		c.*63T>C		3_prime_UTR	Exon 9 of 9	NP_005165.1
	ATP5F1C	NM_001320886.2		c.*97T>C		3_prime_UTR	Exon 9 of 9	NP_001307815.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP5F1C	ENST00000356708.12	TSL:1 MANE Select	c.*97T>C		3_prime_UTR	Exon 10 of 10	ENSP00000349142.7
	ATP5F1C	ENST00000335698.4	TSL:1	c.*63T>C		3_prime_UTR	Exon 9 of 9	ENSP00000338568.4
	ATP5F1C	ENST00000465936.5	TSL:3	n.224T>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52876 AN: 151980 Hom.: 9230 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.327

GnomAD4 exome AF: 0.364 AC: 512211 AN: 1405290 Hom.: 94056 Cov.: 25 AF XY: 0.365 AC XY: 255610 AN XY: 699756

African (AFR) AF: 0.313 AC: 9985 AN: 31946

American (AMR) AF: 0.368 AC: 14751 AN: 40068

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 9037 AN: 24938

East Asian (EAS) AF: 0.259 AC: 10109 AN: 39080

South Asian (SAS) AF: 0.426 AC: 33697 AN: 79020

European-Finnish (FIN) AF: 0.347 AC: 18028 AN: 51932

Middle Eastern (MID) AF: 0.330 AC: 1826 AN: 5530

European-Non Finnish (NFE) AF: 0.366 AC: 393844 AN: 1074636

Other (OTH) AF: 0.360 AC: 20934 AN: 58140

GnomAD4 genome AF: 0.348 AC: 52902 AN: 152098 Hom.: 9230 Cov.: 32 AF XY: 0.347 AC XY: 25832 AN XY: 74358

African (AFR) AF: 0.312 AC: 12931 AN: 41490

American (AMR) AF: 0.360 AC: 5496 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1240 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1263 AN: 5182

South Asian (SAS) AF: 0.435 AC: 2097 AN: 4822

European-Finnish (FIN) AF: 0.356 AC: 3760 AN: 10558

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25098 AN: 67980

Other (OTH) AF: 0.327 AC: 691 AN: 2110

Alfa AF: 0.351 Hom.: 24673

Bravo AF: 0.340

Asia WGS AF: 0.369 AC: 1283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.8
DANN	Benign	0.81
PhyloP100		1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4655; hg19: chr10-7849688; COSMIC: COSV59621724;