rs6054383

chr20-6603957-G-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 0.391 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;