rs6103489

Positions:

• chr20-43858564-C-T

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 0.511 in 151,960 control chromosomes in the GnomAD database, including 20,110 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 0.51 (20110 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 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: 0.510 AC: 77488 AN: 151842 Hom.: 20069 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.511 AC: 77580 AN: 151960 Hom.: 20110 Cov.: 31 AF XY: 0.516 AC XY: 38334 AN XY: 74266

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.499

Alfa AF: 0.473 Hom.: 3477

Bravo AF: 0.518

Asia WGS AF: 0.582 AC: 2021 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6103489; hg19: chr20-42487204;