1-46673908-C-G

Position:

• chr1-46673908-C-G

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46673908C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATPAF1	ENST00000525633.1	n.-41G>C		upstream_gene_variant		4

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

Gnomad4 AFR exome AF: 0.823

Gnomad4 AMR exome AF: 0.854

Gnomad4 ASJ exome AF: 0.791

Gnomad4 EAS exome AF: 0.939

Gnomad4 SAS exome AF: 0.719

Gnomad4 FIN exome AF: 0.787

Gnomad4 NFE exome AF: 0.766

Gnomad4 OTH exome AF: 0.820

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

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.823

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs601060; hg19: chr1-47139580;