rs286388

Variant names:

• chr5-35580308-T-C
• rs286388

Your query was ambiguous. Multiple possible variants found:

• chr5-35580308-T-C
• chr5-35580308-T-G

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 0.426 in 151,804 control chromosomes in the GnomAD database, including 15,466 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 (15466 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64631 AN: 151686 Hom.: 15431 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.415

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: 0.426 AC: 64717 AN: 151804 Hom.: 15466 Cov.: 31 AF XY: 0.426 AC XY: 31635 AN XY: 74186

African (AFR) AF: 0.657 AC: 27154 AN: 41334

American (AMR) AF: 0.309 AC: 4706 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3472

East Asian (EAS) AF: 0.189 AC: 977 AN: 5180

South Asian (SAS) AF: 0.352 AC: 1698 AN: 4820

European-Finnish (FIN) AF: 0.409 AC: 4284 AN: 10482

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23376 AN: 67946

Other (OTH) AF: 0.386 AC: 815 AN: 2112

Alfa AF: 0.353 Hom.: 5205

Bravo AF: 0.425

Asia WGS AF: 0.310 AC: 1074 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.73
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs286388; hg19: chr5-35580410;