rs1882646

Positions:

• chr2-10891662-A-G

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 0.299 in 152,162 control chromosomes in the GnomAD database, including 10,822 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 0.30 (10822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45438 AN: 152044 Hom.: 10776 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.299 AC: 45543 AN: 152162 Hom.: 10822 Cov.: 32 AF XY: 0.295 AC XY: 21931 AN XY: 74374

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.266

Alfa AF: 0.171 Hom.: 5841

Bravo AF: 0.317

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882646; hg19: chr2-11031788;