rs17759555

Variant names:

• chr17-45340629-C-A
• rs17759555

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 0.222 in 151,712 control chromosomes in the GnomAD database, including 4,501 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 0.22 (4501 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 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: 0.222 AC: 33616 AN: 151594 Hom.: 4502 Cov.: 30

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.222 AC: 33610 AN: 151712 Hom.: 4501 Cov.: 30 AF XY: 0.221 AC XY: 16361 AN XY: 74100

African (AFR) AF: 0.0912 AC: 3776 AN: 41408

American (AMR) AF: 0.194 AC: 2955 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3468

East Asian (EAS) AF: 0.0852 AC: 440 AN: 5164

South Asian (SAS) AF: 0.332 AC: 1591 AN: 4798

European-Finnish (FIN) AF: 0.310 AC: 3248 AN: 10484

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20033 AN: 67856

Other (OTH) AF: 0.217 AC: 456 AN: 2100

Alfa AF: 0.270 Hom.: 14198

Bravo AF: 0.209

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.020
DANN	Benign	0.19
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs17759555; hg19: chr17-43417995;