rs482843

Variant names:

• chr1-70406697-A-G
• rs482843

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 0.516 in 151,946 control chromosomes in the GnomAD database, including 21,358 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 0.52 (21358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.597 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: 0.516 AC: 78360 AN: 151830 Hom.: 21363 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.516 AC: 78369 AN: 151946 Hom.: 21358 Cov.: 32 AF XY: 0.515 AC XY: 38245 AN XY: 74238

African (AFR) AF: 0.357 AC: 14828 AN: 41502

American (AMR) AF: 0.563 AC: 8602 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1893 AN: 3466

East Asian (EAS) AF: 0.304 AC: 1571 AN: 5174

South Asian (SAS) AF: 0.436 AC: 2098 AN: 4816

European-Finnish (FIN) AF: 0.639 AC: 6714 AN: 10514

Middle Eastern (MID) AF: 0.462 AC: 134 AN: 290

European-Non Finnish (NFE) AF: 0.602 AC: 40883 AN: 67898

Other (OTH) AF: 0.507 AC: 1070 AN: 2112

Alfa AF: 0.556 Hom.: 2963

Bravo AF: 0.507

Asia WGS AF: 0.364 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.47
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs482843; hg19: chr1-70872380;