20-48584971-A-G

Position:

• chr20-48584971-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 0.57 in 152,124 control chromosomes in the GnomAD database, including 26,827 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 0.57 (26827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.993

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 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: 0.570 AC: 86594 AN: 152006 Hom.: 26771 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.570 AC: 86706 AN: 152124 Hom.: 26827 Cov.: 32 AF XY: 0.571 AC XY: 42448 AN XY: 74338

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.569

Alfa AF: 0.459 Hom.: 21306

Bravo AF: 0.583

Asia WGS AF: 0.614 AC: 2132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6019300; hg19: chr20-47201509;