rs2489260

Positions:

• 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/exons	MANE	UniProt

Ensembl

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