rs17661089

Variant names:

• chr5-56810169-A-G
• rs17661089

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 0.0577 in 152,308 control chromosomes in the GnomAD database, including 355 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 0.058 (355 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0577 AC: 8786 AN: 152190 Hom.: 355 Cov.: 33

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0577 AC: 8788 AN: 152308 Hom.: 355 Cov.: 33 AF XY: 0.0597 AC XY: 4446 AN XY: 74472

African (AFR) AF: 0.0136 AC: 567 AN: 41568

American (AMR) AF: 0.0485 AC: 743 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3470

East Asian (EAS) AF: 0.0150 AC: 78 AN: 5190

South Asian (SAS) AF: 0.152 AC: 733 AN: 4824

European-Finnish (FIN) AF: 0.0664 AC: 704 AN: 10608

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0798 AC: 5426 AN: 68020

Other (OTH) AF: 0.0597 AC: 126 AN: 2112

Alfa AF: 0.0637 Hom.: 402

Bravo AF: 0.0519

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.31
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs17661089; hg19: chr5-56105996;