rs2082107

Variant names:

• chr10-43073058-A-G
• rs2082107

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 0.435 in 151,942 control chromosomes in the GnomAD database, including 14,490 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 0.43 (14490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

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 = 0.476 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: 0.435 AC: 66013 AN: 151824 Hom.: 14463 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.435 AC: 66090 AN: 151942 Hom.: 14490 Cov.: 32 AF XY: 0.434 AC XY: 32211 AN XY: 74246

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.423

Alfa AF: 0.425 Hom.: 1710

Bravo AF: 0.444

Asia WGS AF: 0.373 AC: 1297 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	1.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2082107; hg19: chr10-43568506;