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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.690

Alfa AF: 0.674 Hom.: 55219

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2460000; hg19: chr1-2156362;