rs6024731

Variant names:

• chr20-56246360-A-G
• rs6024731

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 0.319 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.485 AC: 20102 AN: 41424

American (AMR) AF: 0.210 AC: 3204 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1083 AN: 3464

East Asian (EAS) AF: 0.293 AC: 1510 AN: 5152

South Asian (SAS) AF: 0.305 AC: 1471 AN: 4816

European-Finnish (FIN) AF: 0.247 AC: 2616 AN: 10574

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17596 AN: 67960

Other (OTH) AF: 0.284 AC: 597 AN: 2104

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
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6024731; hg19: chr20-54821416;