rs6045803

Variant names:

• chr20-19067989-A-C
• rs6045803

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 0.418 in 152,034 control chromosomes in the GnomAD database, including 14,055 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 0.42 (14055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

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 (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63584 AN: 151914 Hom.: 14040 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.418 AC: 63619 AN: 152034 Hom.: 14055 Cov.: 32 AF XY: 0.419 AC XY: 31145 AN XY: 74308

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.423

Alfa AF: 0.474 Hom.: 35905

Bravo AF: 0.400

Asia WGS AF: 0.349 AC: 1213 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	8.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6045803; hg19: chr20-19048633;