NM_001394565.1:c.540+571T>C

Variant names:

• chr1-46653246-A-G
• rs1150068
• NM_001394565.1:c.540+571T>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.540+571T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,830 control chromosomes in the GnomAD database, including 15,555 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 0.42 (15555 hom., cov: 31)
• Consequence: ATPAF1 NM_001394565.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATPAF1	NM_001394565.1	c.540+571T>C		intron_variant	Intron 5 of 8	ENST00000574428.6	NP_001381494.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATPAF1	ENST00000574428.6	c.540+571T>C		intron_variant	Intron 5 of 8	1	NM_001394565.1	ENSP00000459167.2

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63270 AN: 151712 Hom.: 15483 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.418 AC: 63407 AN: 151830 Hom.: 15555 Cov.: 31 AF XY: 0.424 AC XY: 31419 AN XY: 74174

African (AFR) AF: 0.644 AC: 26669 AN: 41388

American (AMR) AF: 0.457 AC: 6955 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3468

East Asian (EAS) AF: 0.778 AC: 3997 AN: 5136

South Asian (SAS) AF: 0.408 AC: 1965 AN: 4812

European-Finnish (FIN) AF: 0.293 AC: 3085 AN: 10524

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18256 AN: 67970

Other (OTH) AF: 0.427 AC: 901 AN: 2108

Alfa AF: 0.356 Hom.: 1449

Bravo AF: 0.441

Asia WGS AF: 0.609 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.97
DANN	Benign	0.41
PhyloP100		-0.17
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: rs1150068; hg19: chr1-47118918;