20-48468674-G-A

Position:

• chr20-48468674-G-A

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 0.379 in 151,958 control chromosomes in the GnomAD database, including 11,847 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 0.38 (11847 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

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 (AFR) allele frequency at 95% confidence interval = 0.505 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: 0.378 AC: 57453 AN: 151840 Hom.: 11812 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.379 AC: 57540 AN: 151958 Hom.: 11847 Cov.: 32 AF XY: 0.386 AC XY: 28654 AN XY: 74244

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.326

Alfa AF: 0.292 Hom.: 5431

Bravo AF: 0.395

Asia WGS AF: 0.405 AC: 1408 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	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6019216; hg19: chr20-47096920;