rs17762006

Variant names:

• chr20-16829128-A-C
• rs17762006

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0341 in 152,256 control chromosomes in the GnomAD database, including 95 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 0.034 (95 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0341 (5185/152256) while in subpopulation AFR AF = 0.0428 (1776/41530). AF 95% confidence interval is 0.0411. There are 95 homozygotes in GnomAd4. There are 2376 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 95 gene

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: 0.0340 AC: 5169 AN: 152138 Hom.: 95 Cov.: 33

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0174

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0260

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0362

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0341 AC: 5185 AN: 152256 Hom.: 95 Cov.: 33 AF XY: 0.0319 AC XY: 2376 AN XY: 74454

African (AFR) AF: 0.0428 AC: 1776 AN: 41530

American (AMR) AF: 0.0173 AC: 265 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3472

East Asian (EAS) AF: 0.00829 AC: 43 AN: 5184

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4822

European-Finnish (FIN) AF: 0.0260 AC: 276 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0362 AC: 2460 AN: 68028

Other (OTH) AF: 0.0265 AC: 56 AN: 2114

Alfa AF: 0.0358 Hom.: 17

Bravo AF: 0.0337

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.28
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs17762006; hg19: chr20-16809773;