rs629412

chr1-46655001-A-Gchr1-46655001-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394565.1(ATPAF1):c.490-1134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,148 control chromosomes in the GnomAD database, including 3,830 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 0.14 (3830 hom., cov: 31)
• Consequence: ATPAF1 NM_001394565.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

ATPAF1 (HGNC:18803): (ATP synthase mitochondrial F1 complex assembly factor 1) This gene encodes an assembly factor for the F(1) component of the mitochondrial ATP synthase. This protein binds specifically to the F1 beta subunit and is thought to prevent this subunit from forming nonproductive homooligomers during enzyme assembly. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATPAF1	NM_001394565.1	c.490-1134T>C		intron_variant		ENST00000574428.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATPAF1	ENST00000574428.6	c.490-1134T>C		intron_variant		1	NM_001394565.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21248 AN: 152032 Hom.: 3809 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0377

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00540

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.140 AC: 21326 AN: 152148 Hom.: 3830 Cov.: 31 AF XY: 0.143 AC XY: 10602 AN XY: 74380

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.0721

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0377

Gnomad4 NFE AF: 0.00538

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0394 Hom.: 128

Bravo AF: 0.153

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.4
Dann	Benign	0.56

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

Other links and lift over

dbSNP: rs629412; hg19: chr1-47120673;