rs9380825

Positions:

• chr6-39043187-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 0.246 in 152,184 control chromosomes in the GnomAD database, including 5,718 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 0.25 (5718 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.928

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37390 AN: 152066 Hom.: 5718 Cov.: 33

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.246 AC: 37393 AN: 152184 Hom.: 5718 Cov.: 33 AF XY: 0.244 AC XY: 18177 AN XY: 74390

Gnomad4 AFR AF: 0.0720

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.244

Alfa AF: 0.298 Hom.: 2238

Bravo AF: 0.233

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380825; hg19: chr6-39010963;