rs209181

Variant names:

• chr6-28824700-G-A
• rs209181

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 0.126 in 151,986 control chromosomes in the GnomAD database, including 1,307 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 0.13 (1307 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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: 0.126 AC: 19075 AN: 151868 Hom.: 1306 Cov.: 30

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.0827

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.126 AC: 19086 AN: 151986 Hom.: 1307 Cov.: 30 AF XY: 0.120 AC XY: 8913 AN XY: 74292

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0692

Gnomad4 ASJ AF: 0.0779

Gnomad4 EAS AF: 0.0200

Gnomad4 SAS AF: 0.0825

Gnomad4 FIN AF: 0.0813

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.110

Alfa AF: 0.133 Hom.: 1073

Bravo AF: 0.127

Asia WGS AF: 0.0550 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	4.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs209181; hg19: chr6-28792477;