chr20-17788895-G-A

Variant names:

• chr20-17788895-G-A
• rs4814656

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 0.387 in 151,836 control chromosomes in the GnomAD database, including 11,952 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 0.39 (11952 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 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: 0.387 AC: 58692 AN: 151718 Hom.: 11947 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.387 AC: 58733 AN: 151836 Hom.: 11952 Cov.: 31 AF XY: 0.391 AC XY: 29039 AN XY: 74196

African (AFR) AF: 0.282 AC: 11652 AN: 41378

American (AMR) AF: 0.391 AC: 5962 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1994 AN: 5170

South Asian (SAS) AF: 0.349 AC: 1680 AN: 4810

European-Finnish (FIN) AF: 0.566 AC: 5954 AN: 10518

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29212 AN: 67920

Other (OTH) AF: 0.373 AC: 785 AN: 2104

Alfa AF: 0.397 Hom.: 4128

Bravo AF: 0.370

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.76
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4814656; hg19: chr20-17769540;