rs2425764

Variant names:

• chr20-46171806-A-G
• rs2425764

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 0.197 in 152,168 control chromosomes in the GnomAD database, including 3,131 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 0.20 (3131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29896 AN: 152050 Hom.: 3123 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.197 AC: 29948 AN: 152168 Hom.: 3131 Cov.: 32 AF XY: 0.197 AC XY: 14637 AN XY: 74380

African (AFR) AF: 0.260 AC: 10808 AN: 41508

American (AMR) AF: 0.166 AC: 2546 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3468

East Asian (EAS) AF: 0.0251 AC: 130 AN: 5188

South Asian (SAS) AF: 0.0802 AC: 387 AN: 4826

European-Finnish (FIN) AF: 0.238 AC: 2517 AN: 10568

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12479 AN: 67994

Other (OTH) AF: 0.191 AC: 404 AN: 2116

Alfa AF: 0.182 Hom.: 3186

Bravo AF: 0.193

Asia WGS AF: 0.102 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.58
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2425764; hg19: chr20-44800445;