20-45925376-T-C

Variant names:

• chr20-45925376-T-C
• rs6065906

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 0.166 in 152,070 control chromosomes in the GnomAD database, including 2,168 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 0.17 (2168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 99 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25219 AN: 151952 Hom.: 2163 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.166 AC: 25245 AN: 152070 Hom.: 2168 Cov.: 32 AF XY: 0.165 AC XY: 12283 AN XY: 74330

African (AFR) AF: 0.161 AC: 6692 AN: 41482

American (AMR) AF: 0.131 AC: 1999 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3470

East Asian (EAS) AF: 0.0238 AC: 123 AN: 5172

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4818

European-Finnish (FIN) AF: 0.150 AC: 1587 AN: 10602

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12636 AN: 67942

Other (OTH) AF: 0.161 AC: 339 AN: 2106

Alfa AF: 0.173 Hom.: 7236

Bravo AF: 0.163

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6065906; hg19: chr20-44554015;