rs6024730

Variant names:

• chr20-56245733-G-A
• rs6024730

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 0.249 in 152,162 control chromosomes in the GnomAD database, including 5,260 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 0.25 (5260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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: 0.249 AC: 37880 AN: 152044 Hom.: 5247 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.249 AC: 37933 AN: 152162 Hom.: 5260 Cov.: 32 AF XY: 0.249 AC XY: 18514 AN XY: 74402

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.212

Alfa AF: 0.208 Hom.: 2060

Bravo AF: 0.249

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6024730; hg19: chr20-54820789;