20-32811070-A-G

Position:

• chr20-32811070-A-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 0.247 in 152,016 control chromosomes in the GnomAD database, including 5,078 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 0.25 (5078 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 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: 0.247 AC: 37498 AN: 151896 Hom.: 5068 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.247 AC: 37531 AN: 152016 Hom.: 5078 Cov.: 31 AF XY: 0.249 AC XY: 18510 AN XY: 74286

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.244

Alfa AF: 0.226 Hom.: 4052

Bravo AF: 0.255

Asia WGS AF: 0.441 AC: 1531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	15
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8118663; hg19: chr20-31398876;