1-247459055-A-G

Variant names:

• chr1-247459055-A-G
• rs10733113

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 0.819 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.845

Alfa AF: 0.841 Hom.: 25555

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10733113; hg19: chr1-247622357;