chr20-25101620-G-A

Variant names:

• chr20-25101620-G-A
• rs2224072

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 0.829 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.826 AC: 34303 AN: 41518

American (AMR) AF: 0.868 AC: 13279 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2898 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5167 AN: 5178

South Asian (SAS) AF: 0.914 AC: 4405 AN: 4818

European-Finnish (FIN) AF: 0.823 AC: 8715 AN: 10594

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54539 AN: 68014

Other (OTH) AF: 0.851 AC: 1800 AN: 2116

Alfa AF: 0.814 Hom.: 6159

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2224072; hg19: chr20-25082256;