20-5901916-G-A

Position:

• chr20-5901916-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 0.448 in 151,980 control chromosomes in the GnomAD database, including 16,285 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 (16285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 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: 0.448 AC: 67974 AN: 151862 Hom.: 16238 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.448 AC: 68082 AN: 151980 Hom.: 16285 Cov.: 32 AF XY: 0.451 AC XY: 33508 AN XY: 74286

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.422

Alfa AF: 0.408 Hom.: 2003

Bravo AF: 0.452

Asia WGS AF: 0.631 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1287059; hg19: chr20-5882562;