rs17762006

Positions:

• chr20-16829128-A-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 95 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0428

Gnomad4 AMR AF: 0.0173

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.00829

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0260

Gnomad4 NFE AF: 0.0362

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0361 Hom.: 16

Bravo AF: 0.0337

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17762006; hg19: chr20-16809773;