rs6054383

Variant names:

• chr20-6603957-G-T
• rs6054383

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 0.391 in 151,988 control chromosomes in the GnomAD database, including 12,565 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 0.39 (12565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 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: 0.391 AC: 59441 AN: 151870 Hom.: 12552 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.391 AC: 59490 AN: 151988 Hom.: 12565 Cov.: 32 AF XY: 0.396 AC XY: 29451 AN XY: 74290

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.412

Alfa AF: 0.416 Hom.: 20159

Bravo AF: 0.391

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6054383; hg19: chr20-6584604;