chr20-17057618-G-A

Variant names:

• chr20-17057618-G-A
• rs6075165

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 0.342 in 152,160 control chromosomes in the GnomAD database, including 11,107 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 0.34 (11107 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52056 AN: 152040 Hom.: 11104 Cov.: 33

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.342 AC: 52069 AN: 152160 Hom.: 11107 Cov.: 33 AF XY: 0.352 AC XY: 26164 AN XY: 74374

African (AFR) AF: 0.0992 AC: 4122 AN: 41538

American (AMR) AF: 0.468 AC: 7161 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1448 AN: 3472

East Asian (EAS) AF: 0.755 AC: 3892 AN: 5156

South Asian (SAS) AF: 0.516 AC: 2488 AN: 4822

European-Finnish (FIN) AF: 0.464 AC: 4911 AN: 10586

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26951 AN: 67976

Other (OTH) AF: 0.368 AC: 779 AN: 2116

Alfa AF: 0.285 Hom.: 1120

Bravo AF: 0.332

Asia WGS AF: 0.608 AC: 2112 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	1.2
DANN	Benign	0.76
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6075165; hg19: chr20-17038263;