rs6028457

Positions:

• chr20-39489863-A-G
• chr20-39489863-A-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.579 in 152,126 control chromosomes in the GnomAD database, including 25,957 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 0.58 (25957 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.62

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.579 AC: 88030 AN: 152008 Hom.: 25932 Cov.: 33

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.579 AC: 88093 AN: 152126 Hom.: 25957 Cov.: 33 AF XY: 0.577 AC XY: 42933 AN XY: 74360

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.583

Alfa AF: 0.572 Hom.: 4778

Bravo AF: 0.563

Asia WGS AF: 0.482 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	21
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6028457; hg19: chr20-38118506;