rs6024728

Variant names:

• chr20-56243950-A-C
• rs6024728

Your query was ambiguous. Multiple possible variants found:

• chr20-56243950-A-C
• chr20-56243950-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.816 in 151,984 control chromosomes in the GnomAD database, including 50,796 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 0.82 (50796 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.816 AC: 123900 AN: 151866 Hom.: 50740 Cov.: 31

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.816 AC: 124013 AN: 151984 Hom.: 50796 Cov.: 31 AF XY: 0.817 AC XY: 60645 AN XY: 74244

African (AFR) AF: 0.770 AC: 31907 AN: 41452

American (AMR) AF: 0.853 AC: 13030 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2718 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5128 AN: 5136

South Asian (SAS) AF: 0.873 AC: 4195 AN: 4808

European-Finnish (FIN) AF: 0.803 AC: 8473 AN: 10546

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55939 AN: 67986

Other (OTH) AF: 0.810 AC: 1710 AN: 2110

Alfa AF: 0.817 Hom.: 81749

Bravo AF: 0.817

Asia WGS AF: 0.932 AC: 3241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.44
DANN	Benign	0.38
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6024728; hg19: chr20-54819006;