20-43896850-A-G

Variant names:

• chr20-43896850-A-G
• rs11696193

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.277 in 151,878 control chromosomes in the GnomAD database, including 6,197 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 0.28 (6197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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: 0.277 AC: 42010 AN: 151760 Hom.: 6184 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.277 AC: 42041 AN: 151878 Hom.: 6197 Cov.: 32 AF XY: 0.276 AC XY: 20514 AN XY: 74234

African (AFR) AF: 0.282 AC: 11655 AN: 41382

American (AMR) AF: 0.223 AC: 3397 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1361 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2748 AN: 5156

South Asian (SAS) AF: 0.382 AC: 1840 AN: 4816

European-Finnish (FIN) AF: 0.161 AC: 1692 AN: 10524

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18298 AN: 67956

Other (OTH) AF: 0.330 AC: 698 AN: 2114

Alfa AF: 0.268 Hom.: 4835

Bravo AF: 0.280

Asia WGS AF: 0.474 AC: 1648 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	2.3
DANN	Benign	0.20
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11696193; hg19: chr20-42525490;