NM_001394565.1:c.490-1134T>C

Variant names:

• chr1-46655001-A-G
• rs629412
• NM_001394565.1:c.490-1134T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394565.1. 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
	ATPAF1	NM_001394565.1	MANE Select	c.490-1134T>C		intron	N/A	NP_001381494.1
	ATPAF1	NM_022745.6		c.559-1134T>C		intron	N/A	NP_073582.3
	ATPAF1	NM_001042546.2		c.559-1134T>C		intron	N/A	NP_001036011.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATPAF1	ENST00000574428.6	TSL:1 MANE Select	c.490-1134T>C		intron	N/A	ENSP00000459167.2
	ATPAF1	ENST00000576409.5	TSL:1	c.559-1134T>C		intron	N/A	ENSP00000460964.1
	ATPAF1	ENST00000329231.8	TSL:2	c.559-1134T>C		intron	N/A	ENSP00000330685.4

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

African (AFR) AF: 0.396 AC: 16420 AN: 41466

American (AMR) AF: 0.0721 AC: 1102 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2043 AN: 5172

South Asian (SAS) AF: 0.143 AC: 689 AN: 4820

European-Finnish (FIN) AF: 0.0377 AC: 400 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00538 AC: 366 AN: 68012

Other (OTH) AF: 0.115 AC: 244 AN: 2114

Alfa AF: 0.0511 Hom.: 192

Bravo AF: 0.153

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.56
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs629412; hg19: chr1-47120673;