rs9380825

Variant names:

• chr6-39043187-G-A
• rs9380825

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0720 AC: 2993 AN: 41550

American (AMR) AF: 0.254 AC: 3889 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1067 AN: 3470

East Asian (EAS) AF: 0.172 AC: 890 AN: 5182

South Asian (SAS) AF: 0.199 AC: 961 AN: 4824

European-Finnish (FIN) AF: 0.327 AC: 3457 AN: 10576

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23331 AN: 67976

Other (OTH) AF: 0.244 AC: 513 AN: 2106

Alfa AF: 0.298 Hom.: 2794

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
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs9380825; hg19: chr6-39010963;