rs9380069

chr6-28235522-A-G

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 0.127 in 152,198 control chromosomes in the GnomAD database, including 1,300 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 (1300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 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: 0.127 AC: 19380 AN: 152080 Hom.: 1300 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0777

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.127 AC: 19387 AN: 152198 Hom.: 1300 Cov.: 32 AF XY: 0.123 AC XY: 9154 AN XY: 74430

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0863

Gnomad4 FIN AF: 0.0777

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.112

Alfa AF: 0.122 Hom.: 1684

Bravo AF: 0.135

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.53
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380069; hg19: chr6-28203300;