rs6883565

Variant names:

• chr5-13600237-A-T
• rs6883565

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 0.573 in 152,072 control chromosomes in the GnomAD database, including 27,090 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 0.57 (27090 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 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: 0.574 AC: 87162 AN: 151954 Hom.: 27084 Cov.: 33

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.573 AC: 87199 AN: 152072 Hom.: 27090 Cov.: 33 AF XY: 0.569 AC XY: 42324 AN XY: 74322

African (AFR) AF: 0.373 AC: 15481 AN: 41468

American (AMR) AF: 0.682 AC: 10407 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2222 AN: 3470

East Asian (EAS) AF: 0.114 AC: 593 AN: 5182

South Asian (SAS) AF: 0.607 AC: 2928 AN: 4824

European-Finnish (FIN) AF: 0.592 AC: 6249 AN: 10554

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47076 AN: 67996

Other (OTH) AF: 0.603 AC: 1275 AN: 2114

Alfa AF: 0.627 Hom.: 3826

Bravo AF: 0.571

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6883565; hg19: chr5-13600346;