20-48445065-T-C

Position:

• chr20-48445065-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 0.331 in 151,992 control chromosomes in the GnomAD database, including 8,974 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 0.33 (8974 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48445065T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50188 AN: 151872 Hom.: 8958 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.331 AC: 50239 AN: 151992 Hom.: 8974 Cov.: 32 AF XY: 0.333 AC XY: 24748 AN XY: 74308

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.339

Alfa AF: 0.345 Hom.: 1919

Bravo AF: 0.342

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4809696; hg19: chr20-47073807;