rs209181

chr6-28824700-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;