20-25152589-A-G

Position:

• chr20-25152589-A-G

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 0.406 in 151,768 control chromosomes in the GnomAD database, including 14,902 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 0.41 (14902 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 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: 0.406 AC: 61565 AN: 151650 Hom.: 14869 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.406 AC: 61649 AN: 151768 Hom.: 14902 Cov.: 31 AF XY: 0.405 AC XY: 30033 AN XY: 74142

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.383

Alfa AF: 0.311 Hom.: 3862

Bravo AF: 0.430

Asia WGS AF: 0.443 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6050372; hg19: chr20-25133225;