rs2024628

Variant names:

• chr20-40502677-A-G
• rs2024628

Your query was ambiguous. Multiple possible variants found:

• chr20-40502677-A-G
• chr20-40502677-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 0.465 in 152,044 control chromosomes in the GnomAD database, including 17,761 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 0.47 (17761 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 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: 0.465 AC: 70660 AN: 151926 Hom.: 17719 Cov.: 33

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.465 AC: 70748 AN: 152044 Hom.: 17761 Cov.: 33 AF XY: 0.465 AC XY: 34558 AN XY: 74336

African (AFR) AF: 0.652 AC: 27005 AN: 41440

American (AMR) AF: 0.359 AC: 5486 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1341 AN: 3472

East Asian (EAS) AF: 0.625 AC: 3226 AN: 5164

South Asian (SAS) AF: 0.422 AC: 2037 AN: 4822

European-Finnish (FIN) AF: 0.410 AC: 4332 AN: 10572

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25857 AN: 67984

Other (OTH) AF: 0.425 AC: 899 AN: 2116

Alfa AF: 0.412 Hom.: 19002

Bravo AF: 0.469

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs2024628; hg19: chr20-39131317;