chr20-25101620-G-A

Position:

• chr20-25101620-G-A

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 0.829 in 152,208 control chromosomes in the GnomAD database, including 52,498 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 0.83 (52498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126125 AN: 152090 Hom.: 52462 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.829 AC: 126215 AN: 152208 Hom.: 52498 Cov.: 32 AF XY: 0.835 AC XY: 62154 AN XY: 74422

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.851

Alfa AF: 0.814 Hom.: 5904

Bravo AF: 0.832

Asia WGS AF: 0.950 AC: 3302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2224072; hg19: chr20-25082256;