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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.425

Alfa AF: 0.432 Hom.: 3332

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2024628; hg19: chr20-39131317;