rs17535909

Variant names:

• chr5-163528879-G-A
• rs17535909

Your query was ambiguous. Multiple possible variants found:

• chr5-163528879-G-A
• chr5-163528879-G-C

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 0.261 in 151,896 control chromosomes in the GnomAD database, including 5,459 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 0.26 (5459 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 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: 0.261 AC: 39620 AN: 151778 Hom.: 5454 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.261 AC: 39642 AN: 151896 Hom.: 5459 Cov.: 31 AF XY: 0.253 AC XY: 18784 AN XY: 74234

African (AFR) AF: 0.218 AC: 9036 AN: 41412

American (AMR) AF: 0.275 AC: 4202 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3462

East Asian (EAS) AF: 0.105 AC: 539 AN: 5136

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4818

European-Finnish (FIN) AF: 0.136 AC: 1429 AN: 10544

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21145 AN: 67932

Other (OTH) AF: 0.269 AC: 568 AN: 2110

Alfa AF: 0.292 Hom.: 15415

Bravo AF: 0.271

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.44
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs17535909; hg19: chr5-162955885;