20-48249703-T-C

Position:

• chr20-48249703-T-C

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 0.9 in 152,132 control chromosomes in the GnomAD database, including 61,723 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 0.90 (61723 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48249703T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136757 AN: 152014 Hom.: 61674 Cov.: 30

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.900 AC: 136864 AN: 152132 Hom.: 61723 Cov.: 30 AF XY: 0.901 AC XY: 66974 AN XY: 74368

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.895

Alfa AF: 0.908 Hom.: 11767

Bravo AF: 0.897

Asia WGS AF: 0.892 AC: 3102 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	0.076
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs226844; hg19: chr20-46878446;