rs2010809

Positions:

• chr20-43362961-C-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 0.0727 in 150,900 control chromosomes in the GnomAD database, including 996 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 0.073 (996 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.917

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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: 0.0726 AC: 10949 AN: 150808 Hom.: 995 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0289

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0124

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0727 AC: 10970 AN: 150900 Hom.: 996 Cov.: 31 AF XY: 0.0712 AC XY: 5240 AN XY: 73638

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0291

Gnomad4 ASJ AF: 0.0289

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0639

Gnomad4 FIN AF: 0.0124

Gnomad4 NFE AF: 0.0113

Gnomad4 OTH AF: 0.0562

Alfa AF: 0.0469 Hom.: 68

Bravo AF: 0.0795

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2010809; hg19: chr20-41991601;