rs502716

Variant names:

• chr20-945754-G-A
• rs502716

Your query was ambiguous. Multiple possible variants found:

• chr20-945754-G-A
• chr20-945754-G-C
• chr20-945754-G-T

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 0.292 in 152,176 control chromosomes in the GnomAD database, including 7,182 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 0.29 (7182 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 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: 0.292 AC: 44442 AN: 152058 Hom.: 7184 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.292 AC: 44459 AN: 152176 Hom.: 7182 Cov.: 33 AF XY: 0.287 AC XY: 21388 AN XY: 74396

African (AFR) AF: 0.165 AC: 6858 AN: 41534

American (AMR) AF: 0.270 AC: 4131 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3470

East Asian (EAS) AF: 0.283 AC: 1457 AN: 5156

South Asian (SAS) AF: 0.290 AC: 1402 AN: 4830

European-Finnish (FIN) AF: 0.272 AC: 2879 AN: 10588

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24939 AN: 67980

Other (OTH) AF: 0.317 AC: 670 AN: 2116

Alfa AF: 0.345 Hom.: 29678

Bravo AF: 0.288

Asia WGS AF: 0.300 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.51
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs502716; hg19: chr20-926397;