20-48450711-A-G

Position:

• chr20-48450711-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 0.577 in 151,962 control chromosomes in the GnomAD database, including 26,467 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 0.58 (26467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.577 AC: 87617 AN: 151844 Hom.: 26408 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.577 AC: 87732 AN: 151962 Hom.: 26467 Cov.: 32 AF XY: 0.582 AC XY: 43178 AN XY: 74244

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.550

Alfa AF: 0.485 Hom.: 7810

Bravo AF: 0.599

Asia WGS AF: 0.644 AC: 2239 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	0.070
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926693; hg19: chr20-47078957;