1-46673908-C-G

Variant names:

• chr1-46673908-C-G
• rs601060
• ENST00000418985.2:n.-152C>G

Variant summary

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

The ENST00000418985.2(EFCAB14-AS1):​n.-152C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 158,430 control chromosomes in the GnomAD database, including 50,525 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 0.80 (48606 hom., cov: 33)
  • Exomes 𝑓: 0.79 (1919 hom.)
• Consequence: EFCAB14-AS1 ENST00000418985.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 7 publications found

Genes affected

EFCAB14-AS1 (HGNC:44108): (EFCAB14 antisense RNA 1)

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418985.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB14-AS1	NR_038827.1		n.-128C>G		upstream_gene	N/A
	EFCAB14-AS1	NR_038828.1		n.-128C>G		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB14-AS1	ENST00000418985.2	TSL:3	n.-152C>G		upstream_gene	N/A
	EFCAB14-AS1	ENST00000442839.5	TSL:3	n.-128C>G		upstream_gene	N/A
	ATPAF1	ENST00000525633.1	TSL:4	n.-41G>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121367 AN: 152162 Hom.: 48533 Cov.: 33

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.820

GnomAD4 exome AF: 0.786 AC: 4834 AN: 6150 Hom.: 1919 Cov.: 0 AF XY: 0.785 AC XY: 2438 AN XY: 3104

African (AFR) AF: 0.823 AC: 102 AN: 124

American (AMR) AF: 0.854 AC: 782 AN: 916

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 117 AN: 148

East Asian (EAS) AF: 0.939 AC: 124 AN: 132

South Asian (SAS) AF: 0.719 AC: 197 AN: 274

European-Finnish (FIN) AF: 0.787 AC: 126 AN: 160

Middle Eastern (MID) AF: 0.909 AC: 20 AN: 22

European-Non Finnish (NFE) AF: 0.766 AC: 3125 AN: 4080

Other (OTH) AF: 0.820 AC: 241 AN: 294

GnomAD4 genome AF: 0.798 AC: 121497 AN: 152280 Hom.: 48606 Cov.: 33 AF XY: 0.801 AC XY: 59618 AN XY: 74464

African (AFR) AF: 0.816 AC: 33893 AN: 41560

American (AMR) AF: 0.866 AC: 13238 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2704 AN: 3472

East Asian (EAS) AF: 0.913 AC: 4739 AN: 5192

South Asian (SAS) AF: 0.728 AC: 3515 AN: 4830

European-Finnish (FIN) AF: 0.775 AC: 8213 AN: 10594

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52545 AN: 68020

Other (OTH) AF: 0.823 AC: 1738 AN: 2112

Alfa AF: 0.736 Hom.: 2507

Bravo AF: 0.806

Asia WGS AF: 0.820 AC: 2853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.66
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs601060; hg19: chr1-47139580;