rs2460000

Variant names:

• chr1-2224923-A-G
• rs2460000

Your query was ambiguous. Multiple possible variants found:

• chr1-2224923-A-G
• chr1-2224923-A-T

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 0.702 in 152,206 control chromosomes in the GnomAD database, including 37,900 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 0.70 (37900 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.834 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: 0.702 AC: 106800 AN: 152086 Hom.: 37855 Cov.: 34

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.702 AC: 106900 AN: 152206 Hom.: 37900 Cov.: 34 AF XY: 0.704 AC XY: 52403 AN XY: 74398

African (AFR) AF: 0.768 AC: 31907 AN: 41528

American (AMR) AF: 0.714 AC: 10917 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3470

East Asian (EAS) AF: 0.781 AC: 4047 AN: 5182

South Asian (SAS) AF: 0.856 AC: 4134 AN: 4832

European-Finnish (FIN) AF: 0.629 AC: 6666 AN: 10604

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 45002 AN: 67974

Other (OTH) AF: 0.690 AC: 1461 AN: 2116

Alfa AF: 0.682 Hom.: 97207

Bravo AF: 0.708

Asia WGS AF: 0.792 AC: 2755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.2
DANN	Benign	0.41
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs2460000; hg19: chr1-2156362;