rs2099803

Variant names:

• chr10-107616211-T-A
• rs2099803

Your query was ambiguous. Multiple possible variants found:

• chr10-107616211-T-A
• chr10-107616211-T-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 0.447 in 151,914 control chromosomes in the GnomAD database, including 15,743 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 0.45 (15743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 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: 0.448 AC: 67977 AN: 151796 Hom.: 15746 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.447 AC: 67979 AN: 151914 Hom.: 15743 Cov.: 31 AF XY: 0.443 AC XY: 32872 AN XY: 74254

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.452

Alfa AF: 0.482 Hom.: 2250

Bravo AF: 0.442

Asia WGS AF: 0.261 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2099803; hg19: chr10-109375969;