rs6883565

Positions:

• chr5-13600237-A-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 0.573 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.13600237A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;