rs6883565

Variant names:

• chr5-13600237-A-T
• rs6883565

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 0.573 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.574 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

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.603

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6883565; hg19: chr5-13600346;