20-48554800-A-G

Position:

• chr20-48554800-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 0.685 in 151,986 control chromosomes in the GnomAD database, including 35,886 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 0.68 (35886 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48554800A>G		intergenic_region
LOC105372646	XR_936817.4	n.342+8483T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103923 AN: 151868 Hom.: 35832 Cov.: 30

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.685 AC: 104038 AN: 151986 Hom.: 35886 Cov.: 30 AF XY: 0.685 AC XY: 50872 AN XY: 74268

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.669

Alfa AF: 0.694 Hom.: 75187

Bravo AF: 0.686

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883888; hg19: chr20-47171338;