1-247459055-A-G

Variant names:

• chr1-247459055-A-G
• rs10733113

Variant summary

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

The variant allele was found at a frequency of 0.819 in 151,602 control chromosomes in the GnomAD database, including 51,095 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 0.82 (51095 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 43 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124113 AN: 151484 Hom.: 51065 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.819 AC: 124199 AN: 151602 Hom.: 51095 Cov.: 31 AF XY: 0.820 AC XY: 60714 AN XY: 74082

African (AFR) AF: 0.733 AC: 30275 AN: 41316

American (AMR) AF: 0.868 AC: 13226 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2815 AN: 3466

East Asian (EAS) AF: 0.935 AC: 4821 AN: 5156

South Asian (SAS) AF: 0.917 AC: 4421 AN: 4820

European-Finnish (FIN) AF: 0.793 AC: 8326 AN: 10504

Middle Eastern (MID) AF: 0.866 AC: 253 AN: 292

European-Non Finnish (NFE) AF: 0.850 AC: 57603 AN: 67802

Other (OTH) AF: 0.845 AC: 1784 AN: 2112

Alfa AF: 0.843 Hom.: 34681

Bravo AF: 0.820

Asia WGS AF: 0.906 AC: 3153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.34
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10733113; hg19: chr1-247622357;