5-35578359-G-A

Variant names:

• chr5-35578359-G-A
• rs169587

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 0.427 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.658 AC: 27261 AN: 41438

American (AMR) AF: 0.309 AC: 4721 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3468

East Asian (EAS) AF: 0.189 AC: 975 AN: 5164

South Asian (SAS) AF: 0.354 AC: 1702 AN: 4810

European-Finnish (FIN) AF: 0.412 AC: 4337 AN: 10514

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23387 AN: 67892

Other (OTH) AF: 0.386 AC: 815 AN: 2110

Alfa AF: 0.368 Hom.: 33276

Bravo AF: 0.425

Asia WGS AF: 0.310 AC: 1076 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.9
DANN	Benign	0.85
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs169587; hg19: chr5-35578461;