20-4105891-A-G

Variant names:

• chr20-4105891-A-G
• rs2326373

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 0.851 in 152,064 control chromosomes in the GnomAD database, including 55,283 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 0.85 (55283 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.851 AC: 129372 AN: 151946 Hom.: 55250 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.851 AC: 129461 AN: 152064 Hom.: 55283 Cov.: 31 AF XY: 0.856 AC XY: 63653 AN XY: 74332

African (AFR) AF: 0.801 AC: 33241 AN: 41480

American (AMR) AF: 0.903 AC: 13806 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3083 AN: 3470

East Asian (EAS) AF: 0.960 AC: 4944 AN: 5152

South Asian (SAS) AF: 0.918 AC: 4431 AN: 4826

European-Finnish (FIN) AF: 0.867 AC: 9165 AN: 10566

Middle Eastern (MID) AF: 0.918 AC: 268 AN: 292

European-Non Finnish (NFE) AF: 0.851 AC: 57874 AN: 67970

Other (OTH) AF: 0.873 AC: 1843 AN: 2110

Alfa AF: 0.843 Hom.: 26964

Bravo AF: 0.852

Asia WGS AF: 0.935 AC: 3249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.68
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2326373; hg19: chr20-4086538;