chr20-32814411-G-A

Position:

• chr20-32814411-G-A

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 0.478 in 152,126 control chromosomes in the GnomAD database, including 18,199 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 0.48 (18199 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72623 AN: 152008 Hom.: 18176 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.478 AC: 72697 AN: 152126 Hom.: 18199 Cov.: 33 AF XY: 0.475 AC XY: 35290 AN XY: 74352

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.447

Alfa AF: 0.404 Hom.: 10091

Bravo AF: 0.491

Asia WGS AF: 0.613 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs853858; hg19: chr20-31402217;