rs13209281

Variant names:

• chr6-86434931-A-C
• rs13209281

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 0.0581 in 152,238 control chromosomes in the GnomAD database, including 382 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 0.058 (382 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 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: 0.0581 AC: 8845 AN: 152120 Hom.: 383 Cov.: 33

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0653

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0775

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

GnomAD4 genome AF: 0.0581 AC: 8844 AN: 152238 Hom.: 382 Cov.: 33 AF XY: 0.0592 AC XY: 4405 AN XY: 74436

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.0652

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0664

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0583 Hom.: 32

Bravo AF: 0.0543

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13209281; hg19: chr6-87144649;