rs2082106

Variant names:

• chr10-43036583-C-G
• rs2082106

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 0.691 in 152,116 control chromosomes in the GnomAD database, including 36,688 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 0.69 (36688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 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: 0.691 AC: 104957 AN: 151998 Hom.: 36631 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.691 AC: 105075 AN: 152116 Hom.: 36688 Cov.: 32 AF XY: 0.688 AC XY: 51143 AN XY: 74344

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.666

Alfa AF: 0.684 Hom.: 4457

Bravo AF: 0.685

Asia WGS AF: 0.641 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2082106; hg19: chr10-43532031;