rs2489260

Variant names:

• chr1-12681229-G-A
• rs2489260

Your query was ambiguous. Multiple possible variants found:

• chr1-12681229-G-A
• chr1-12681229-G-C
• chr1-12681229-G-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 0.201 in 126,776 control chromosomes in the GnomAD database, including 4,198 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 0.20 (4198 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.200 AC: 25402 AN: 126720 Hom.: 4170 Cov.: 26

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.201 AC: 25459 AN: 126776 Hom.: 4198 Cov.: 26 AF XY: 0.201 AC XY: 12269 AN XY: 61070

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.0789

Gnomad4 OTH AF: 0.189

Alfa AF: 0.103 Hom.: 2083

Bravo AF: 0.220

Asia WGS AF: 0.241 AC: 836 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2489260; hg19: chr1-12741240;