20-58088218-T-C

Variant names:

• chr20-58088218-T-C
• rs6070346

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 0.298 in 152,180 control chromosomes in the GnomAD database, including 8,512 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 0.30 (8512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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: 0.298 AC: 45301 AN: 152062 Hom.: 8518 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.298 AC: 45279 AN: 152180 Hom.: 8512 Cov.: 32 AF XY: 0.289 AC XY: 21526 AN XY: 74418

African (AFR) AF: 0.105 AC: 4352 AN: 41536

American (AMR) AF: 0.285 AC: 4364 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1497 AN: 3470

East Asian (EAS) AF: 0.0524 AC: 271 AN: 5172

South Asian (SAS) AF: 0.123 AC: 592 AN: 4820

European-Finnish (FIN) AF: 0.334 AC: 3537 AN: 10590

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29606 AN: 67982

Other (OTH) AF: 0.321 AC: 678 AN: 2112

Alfa AF: 0.386 Hom.: 36409

Bravo AF: 0.288

Asia WGS AF: 0.0960 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.014
DANN	Benign	0.34
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs6070346; hg19: chr20-56663274;