rs9380215

chr6-31081878-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 0.0674 in 152,124 control chromosomes in the GnomAD database, including 496 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 0.067 (496 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

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 (EAS) allele frequency at 95% confidence interval = 0.203 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: 0.0676 AC: 10272 AN: 152006 Hom.: 501 Cov.: 30

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0722

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0674 AC: 10255 AN: 152124 Hom.: 496 Cov.: 30 AF XY: 0.0698 AC XY: 5192 AN XY: 74358

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.0902

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.0722

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0710 Hom.: 283

Bravo AF: 0.0647

Asia WGS AF: 0.135 AC: 471 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	2.9
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380215; hg19: chr6-31049655;