rs169587

Variant names:

• chr5-35578359-G-A
• rs169587

Your query was ambiguous. Multiple possible variants found:

• chr5-35578359-G-A
• chr5-35578359-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.427 in 151,856 control chromosomes in the GnomAD database, including 15,530 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 0.43 (15530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 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: 0.427 AC: 64818 AN: 151738 Hom.: 15495 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.427 AC: 64904 AN: 151856 Hom.: 15530 Cov.: 32 AF XY: 0.428 AC XY: 31738 AN XY: 74222

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.386

Alfa AF: 0.353 Hom.: 19522

Bravo AF: 0.425

Asia WGS AF: 0.310 AC: 1076 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.9
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs169587; hg19: chr5-35578461;