rs6024731

chr20-56246360-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 0.319 in 151,966 control chromosomes in the GnomAD database, including 8,531 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 0.32 (8531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

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 (AFR) allele frequency at 95% confidence interval = 0.48 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: 0.319 AC: 48399 AN: 151848 Hom.: 8509 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.319 AC: 48471 AN: 151966 Hom.: 8531 Cov.: 32 AF XY: 0.316 AC XY: 23474 AN XY: 74274

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.284

Alfa AF: 0.298 Hom.: 920

Bravo AF: 0.321

Asia WGS AF: 0.317 AC: 1102 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.70
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6024731; hg19: chr20-54821416;