rs803742

Positions:

• chr20-50449059-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 0.49 in 151,068 control chromosomes in the GnomAD database, including 19,661 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 0.49 (19661 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.626 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: 0.490 AC: 74017 AN: 150958 Hom.: 19668 Cov.: 29

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.490 AC: 74038 AN: 151068 Hom.: 19661 Cov.: 29 AF XY: 0.494 AC XY: 36382 AN XY: 73704

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.516

Alfa AF: 0.544 Hom.: 4692

Bravo AF: 0.484

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs803742; hg19: chr20-49065596;