chr20-46102124-G-A

Position:

• chr20-46102124-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 0.202 in 151,790 control chromosomes in the GnomAD database, including 3,415 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 0.20 (3415 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 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: 0.202 AC: 30578 AN: 151672 Hom.: 3406 Cov.: 30

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.202 AC: 30596 AN: 151790 Hom.: 3415 Cov.: 30 AF XY: 0.204 AC XY: 15089 AN XY: 74134

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.197

Alfa AF: 0.149 Hom.: 371

Bravo AF: 0.192

Asia WGS AF: 0.243 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6065924; hg19: chr20-44730763;