rs2460000

chr1-2224923-A-Gchr1-2224923-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;