20-48460486-A-G

Position:

• chr20-48460486-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 0.321 in 152,012 control chromosomes in the GnomAD database, including 8,335 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 0.32 (8335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

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 = 0.505 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: 0.321 AC: 48772 AN: 151894 Hom.: 8321 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.321 AC: 48815 AN: 152012 Hom.: 8335 Cov.: 32 AF XY: 0.330 AC XY: 24534 AN XY: 74300

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.305

Alfa AF: 0.310 Hom.: 3488

Bravo AF: 0.329

Asia WGS AF: 0.406 AC: 1411 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	2.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs910191; hg19: chr20-47088732;